Lipid formulations for nucleic acid delivery

ABSTRACT

The present invention provides novel, stable lipid particles comprising one or more active agents or therapeutic agents, methods of making the lipid particles, and methods of delivering and/or administering the lipid particles. More particularly, the present invention provides stable nucleic acid-lipid particles (SNALP) comprising a nucleic acid (such as one or more interfering RNA), methods of making the SNALP, and methods of delivering and/or administering the SNALP.

CROSS-REFERENCES TO RELATED APPLICATIONS

The present application claims priority to U.S. Provisional ApplicationNo. 61/045,228, filed Apr. 15, 2008, the disclosure of which is hereinincorporated by reference in its entirety for all purposes.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

Not applicable.

NAMES OF PARTIES TO A JOINT RESEARCH AGREEMENT

Not applicable.

REFERENCE TO A “SEQUENCE LISTING”

Not applicable.

BACKGROUND OF THE INVENTION

RNA interference (RNAi) is an evolutionarily conserved process in whichrecognition of double-stranded RNA (dsRNA) ultimately leads toposttranscriptional suppression of gene expression. This suppression ismediated by short dsRNA, also called small interfering RNA (siRNA),which induces specific degradation of mRNA through complementary basepairing. In several model systems, this natural response has beendeveloped into a powerful tool for the investigation of gene function(see, e.g., Elbashir et al., Genes Dev., 15:188-200 (2001); Hammond etal., Nat. Rev. Genet., 2:110-119 (2001)). More recently, it wasdiscovered that introducing synthetic 21-nucleotide dsRNA duplexes intomammalian cells could efficiently silence gene expression.

Although the precise mechanism is still unclear, RNAi provides apotential new approach to downregulate or silence the transcription andtranslation of a gene of interest. For example, it is desirable tomodulate (e.g., reduce) the expression of certain genes for thetreatment of neoplastic disorders such as cancer. It is also desirableto silence the expression of genes associated with liver diseases anddisorders such as hepatitis. It is further desirable to reduce theexpression of certain genes for the treatment of atherosclerosis and itsmanifestations, e.g., hypercholesterolemia, myocardial infarction, andthrombosis.

A safe and effective nucleic acid delivery system is required for RNAito be therapeutically useful. Viral vectors are relatively efficientgene delivery systems, but suffer from a variety of limitations, such asthe potential for reversion to the wild-type as well as immune responseconcerns. As a result, nonviral gene delivery systems are receivingincreasing attention (Worgall et al., Human Gene Therapy, 8:37 (1997);Peeters et al., Human Gene Therapy, 7:1693 (1996); Yei et al., GeneTherapy, 1:192 (1994); Hope et al., Molecular Membrane Biology, 15:1(1998)). Furthermore, viral systems are rapidly cleared from thecirculation, limiting transfection to “first-pass” organs such as thelungs, liver, and spleen. In addition, these systems induce immuneresponses that compromise delivery with subsequent injections.

Plasmid DNA-cationic liposome complexes are currently the most commonlyemployed nonviral gene delivery vehicles (Felgner, Scientific American,276:102 (1997); Chonn et al., Current Opinion in Biotechnology, 6:698(1995)). For instance, cationic liposome complexes made of anamphipathic compound, a neutral lipid, and a detergent for transfectinginsect cells are disclosed in U.S. Pat. No. 6,458,382. Cationic liposomecomplexes are also disclosed in U.S. Patent Publication No. 20030073640.

Cationic liposome complexes are large, poorly defined systems that arenot suited for systemic applications and can elicit considerable toxicside effects (Harrison et al., Biotechniques, 19:816 (1995); Li et al.,The Gene, 4:891 (1997); Tam et al, Gene Ther., 7:1867 (2000)). As large,positively charged aggregates, lipoplexes are rapidly cleared whenadministered in vivo, with highest expression levels observed infirst-pass organs, particularly the lungs (Huang et al., NatureBiotechnology, 15:620 (1997); Templeton et al., Nature Biotechnology,15:647 (1997); Hofland et al., Pharmaceutical Research, 14:742 (1997)).

Other liposomal delivery systems include, for example, the use ofreverse micelles, anionic liposomes, and polymer liposomes. Reversemicelles are disclosed in U.S. Pat. No. 6,429,200. Anionic liposomes aredisclosed in U.S. Patent Publication No. 20030026831. Polymer liposomesthat incorporate dextrin or glycerol-phosphocholine polymers aredisclosed in U.S. Patent Publication Nos. 20020081736 and 20030082103,respectively.

A gene delivery system containing an encapsulated nucleic acid forsystemic delivery should be small (i.e., less than about 100 nmdiameter) and should remain intact in the circulation for an extendedperiod of time in order to achieve delivery to affected tissues. Thisrequires a highly stable, serum-resistant nucleic acid-containingparticle that does not interact with cells and other components of thevascular compartment. The particle should also readily interact withtarget cells at a disease site in order to facilitate intracellulardelivery of a desired nucleic acid.

Recent work has shown that nucleic acids can be encapsulated in small(e.g., about 70 nm diameter) “stabilized plasmid-lipid particles” (SPLP)that consist of a single plasmid encapsulated within a bilayer lipidvesicle (Wheeler et al., Gene Therapy, 6:271 (1999)). These SPLPstypically contain the “fusogenic” lipid dioleoylphosphatidylethanolamine(DOPE), low levels of cationic lipid, and are stabilized in aqueousmedia by the presence of a poly(ethylene glycol) (PEG) coating. SPLPshave systemic application as they exhibit extended circulation lifetimesfollowing intravenous (i.v.) injection, accumulate preferentially atdistal tumor sites due to the enhanced vascular permeability in suchregions, and can mediate transgene expression at these tumor sites. Thelevels of transgene expression observed at the tumor site following i.v.injection of SPLPs containing the luciferase marker gene are superior tothe levels that can be achieved employing plasmid DNA-cationic liposomecomplexes (lipoplexes) or naked DNA.

Thus, there remains a strong need in the art for novel and moreefficient methods and compositions for introducing nucleic acids such assiRNA into cells. In addition, there is a need in the art for methods ofdownregulating the expression of genes of interest to treat or preventdiseases and disorders such as cancer and atherosclerosis. The presentinvention addresses these and other needs.

BRIEF SUMMARY OF THE INVENTION

The present invention provides novel, serum-stable lipid particlescomprising one or more active agents or therapeutic agents, methods ofmaking the lipid particles, and methods of delivering and/oradministering the lipid particles (e.g., for the treatment of a diseaseor disorder).

In preferred embodiments, the active agent or therapeutic agent is fullyencapsulated within the lipid portion of the lipid particle such thatthe active agent or therapeutic agent in the lipid particle is resistantin aqueous solution to enzymatic degradation, e.g., by a nuclease orprotease. In other preferred embodiments, the lipid particles aresubstantially non-toxic to mammals such as humans.

In one aspect, the present invention provides lipid particlescomprising: (a) one or more active agents or therapeutic agents; (b) oneor more cationic lipids comprising from about 50 mol % to about 85 mol %of the total lipid present in the particle; (c) one or more non-cationiclipids comprising from about 13 mol % to about 49.5 mol % of the totallipid present in the particle; and (d) one or more conjugated lipidsthat inhibit aggregation of particles comprising from about 0.5 mol % toabout 2 mol % of the total lipid present in the particle.

More particularly, the present invention provides serum-stable nucleicacid-lipid particles (SNALP) comprising a nucleic acid (e.g., one ormore interfering RNA molecules such as siRNA, aiRNA, and/or miRNA),methods of making the SNALP, and methods of delivering and/oradministering the SNALP (e.g., for the treatment of a disease ordisorder).

In certain embodiments, the nucleic acid-lipid particle (e.g., SNALP)comprises: (a) a nucleic acid (e.g., an interfering RNA); (b) a cationiclipid comprising from about 50 mol % to about 85 mol % of the totallipid present in the particle; (c) a non-cationic lipid comprising fromabout 13 mol % to about 49.5 mol % of the total lipid present in theparticle; and (d) a conjugated lipid that inhibits aggregation ofparticles comprising from about 0.5 mol % to about 2 mol % of the totallipid present in the particle.

In one preferred embodiment, the nucleic acid-lipid particle (e.g.,SNALP) comprises: (a) an siRNA; (b) a cationic lipid comprising fromabout 56.5 mol % to about 66.5 mol % of the total lipid present in theparticle; (c) cholesterol or a derivative thereof comprising from about31.5 mol % to about 42.5 mol % of the total lipid present in theparticle; and (d) a PEG-lipid conjugate comprising from about 1 mol % toabout 2 mol % of the total lipid present in the particle. This preferredembodiment of nucleic acid-lipid particle is generally referred toherein as the “1:62” formulation.

In another preferred embodiment, the nucleic acid-lipid particle (e.g.,SNALP) comprises: (a) an siRNA; (b) a cationic lipid comprising fromabout 52 mol % to about 62 mol % of the total lipid present in theparticle; (c) a mixture of a phospholipid and cholesterol or aderivative thereof comprising from about 36 mol % to about 47 mol % ofthe total lipid present in the particle; and (d) a PEG-lipid conjugatecomprising from about 1 mol % to about 2 mol % of the total lipidpresent in the particle. This preferred embodiment of nucleic acid-lipidparticle is generally referred to herein as the “1:57” formulation.

The present invention also provides pharmaceutical compositionscomprising a lipid particle described herein (e.g., SNALP) and apharmaceutically acceptable carrier.

In another aspect, the present invention provides methods forintroducing an active agent or therapeutic agent (e.g., nucleic acid)into a cell, the method comprising contacting the cell with a lipidparticle described herein such as a nucleic acid-lipid particle (e.g.,SNALP).

In yet another aspect, the present invention provides methods for the invivo delivery of an active agent or therapeutic agent (e.g., nucleicacid), the method comprising administering to a mammalian subject alipid particle described herein such as a nucleic acid-lipid particle(e.g., SNALP).

In a further aspect, the present invention provides methods for treatinga disease or disorder in a mammalian subject in need thereof, the methodcomprising administering to the mammalian subject a therapeuticallyeffective amount of a lipid particle described herein such as a nucleicacid-lipid particle (e.g., SNALP).

Other objects, features, and advantages of the present invention will beapparent to one of skill in the art from the following detaileddescription and figures.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A (Samples 1-8) and FIG. 1B (Samples 9-16) illustrate datademonstrating the activity of 1:57 SNALP containing Eg5 siRNA in a humancolon cancer cell line.

FIG. 2 illustrates data demonstrating the activity of 1:57 SNALPcontaining ApoB siRNA following intravenous administration in mice.

FIG. 3 illustrates additional data demonstrating the activity of 1:57SNALP containing ApoB siRNA following intravenous administration inmice. Each bar represents the group mean of five animals. Error barsindicate the standard deviation.

FIG. 4 illustrates data demonstrating the activity of 1:57 and 1:62SNALP containing ApoB siRNA following intravenous administration inmice.

FIG. 5 illustrates data demonstrating the activity of 1:62 SNALPcontaining ApoB siRNA following intravenous administration in mice.

FIG. 6A (expressed as IU/L) and FIG. 6B (expressed as x-Fold Upper Limitof Normal) illustrate data demonstrating that the tolerability of 1:57SNALP containing ApoB siRNA prepared by citrate buffer versus PBS directdilution did not differ significantly in terms of blood clinicalchemistry parameters.

FIG. 7A (expressed as liver ApoB:GAPD mRNA ratio), FIG. 7B (expressed asrelative plasma ApoB-100 concentration), and FIG. 7C (expressed asplasma total cholesterol) illustrate data demonstrating that theefficacy of 1:57 SNALP containing ApoB siRNA prepared by gear pump wassimilar to the same SNALP prepared by syringe press.

FIG. 8 illustrates data demonstrating that there was very little effecton body weight 24 hours after administration of 1:57 SNALP containingApoB siRNA.

FIG. 9 illustrates data demonstrating that there were no obvious changesin platelet count after administration of 1:57 SNALP containing ApoBsiRNA.

FIG. 10A (expressed as IU/L) and FIG. 10B (expressed as x-Fold UpperLimit of Normal) illustrate data demonstrating that clinicallysignificant liver enzyme elevations (3×ULN) occurred at particular drugdosages of 1:57 SNALP containing ApoB siRNA.

FIG. 11A (expressed as liver ApoB:GAPD mRNA ratio) and FIG. 11B(expressed as relative plasma ApoB-100 concentration) illustrate datademonstrating that the potency of the lower lipid:drug (L:D) 1:57 SNALPcontaining ApoB siRNA was as good as that of the higher L:D SNALP at thetested drug dosages.

FIG. 12 illustrates data demonstrating that ApoB protein and totalcholesterol levels were reduced to a similar extent by 1:57 SNALPcontaining ApoB siRNA at a 6:1 input L:D ratio (final ratio of 7:1) and1:57 SNALP at a 9:1 input L:D ratio (final ratio of 10:1).

FIG. 13 illustrates data demonstrating that a treatment regimen of 1:57SNALP with siRNA targeting PLK-1 is well tolerated with no apparentsigns of treatment related toxicity in mice bearing Hep3B liver tumors.

FIG. 14 illustrates data demonstrating that treatment with 1:57 SNALPcontaining PLK-1 siRNA caused a significant increase in the survival ofHep3B tumor-bearing mice.

FIG. 15 illustrates data demonstrating that treatment with 1:57 SNALPcontaining PLK-1 siRNA reduced PLK-1 mRNA levels by 50% in intrahepaticHep3B tumors growing in mice 24 hours after SNALP administration.

FIG. 16 illustrates data demonstrating that a specific cleavage productof PLK-1 mRNA was detectable by 5′ RACE-PCR in mice treated with 1:57SNALP containing PLK-1 siRNA. 10 μl PCR product/well were loaded onto a1.5% agarose gel. Lane Nos.: (1) molecular weight (MW) marker; (2) PBSmouse 1; (3) PBS mouse 2; (4) PBS mouse 3; (5) Luc SNALP mouse 1; (6)Luc SNALP mouse 2; (7) PLK SNALP mouse 1; (8) PLK SNALP mouse 2; (9) PLKSNALP mouse 3; and (10) no template control.

FIG. 17 illustrates data demonstrating that control (Luc) 1:57SNALP-treated mice displayed normal mitoses in Hep3B tumors (toppanels), whereas mice treated with 1:57 SNALP containing PLK-1 siRNAexhibited numerous aberrant mitoses and tumor cell apoptosis in Hep3Btumors (bottom panels).

FIG. 18 illustrates data demonstrating that multiple doses of 1:57 PLK-1SNALP containing PEG-cDSA induced the regression of established Hep3Bsubcutaneous (S.C.) tumors.

FIG. 19 illustrates data demonstrating PLK-1 mRNA silencing using 1:57PLK SNALP in S.C. Hep3B tumors following a single intravenous SNALPadministration.

FIG. 20 illustrates data demonstrating that PLK-1 PEG-cDSA SNALPinhibited the growth of large S.C. Hep3B tumors.

FIG. 21 illustrates data demonstrating tumor-derived PLK-1 mRNAsilencing in Hep3B intrahepatic tumors.

FIG. 22 illustrates data demonstrating the blood clearance profile of1:57 PLK-1 SNALP containing either PEG-cDMA or PEG-cDSA.

DETAILED DESCRIPTION OF THE INVENTION I. Introduction

The present invention is based, in part, upon the surprising discoverythat lipid particles comprising from about 50 mol % to about 85 mol % ofa cationic lipid, from about 13 mol % to about 49.5 mol % of anon-cationic lipid, and from about 0.5 mol % to about 2 mol % of a lipidconjugate provide advantages when used for the in vitro or in vivodelivery of an active agent, such as a therapeutic nucleic acid (e.g.,an interfering RNA). In particular, as illustrated by the Examplesherein, the present invention provides stable nucleic acid-lipidparticles (SNALP) that advantageously impart increased activity of theencapsulated nucleic acid (e.g., an interfering RNA such as siRNA) andimproved tolerability of the formulations in vivo, resulting in asignificant increase in the therapeutic index as compared to nucleicacid-lipid particle compositions previously described. Additionally, theSNALP of the invention are stable in circulation, e.g., resistant todegradation by nucleases in serum, and are substantially non-toxic tomammals such as humans. As a non-limiting example, FIG. 3 of Example 4shows that one SNALP embodiment of the invention (“1:57 SNALP”) was morethan 10 times as efficacious as compared to a nucleic acid-lipidparticle previously described (“2:30 SNALP”) in mediating target genesilencing at a 10-fold lower dose. Similarly, FIG. 2 of Example 3 showsthat the “1:57 SNALP” formulation was substantially more effective atsilencing the expression of a target gene as compared to nucleicacid-lipid particles previously described (“2:40 SNALP”).

In certain embodiments, the present invention provides improvedcompositions for the delivery of interfering RNA such as siRNAmolecules. In particular, the Examples herein illustrate that theimproved lipid particle formulations of the invention are highlyeffective in downregulating the mRNA and/or protein levels of targetgenes. Furthermore, the Examples herein illustrate that the presence ofcertain molar ratios of lipid components results in improved or enhancedactivity of these lipid particle formulations of the present invention.For instance, the “1:57 SNALP” and “1:62 SNALP” formulations describedherein are exemplary formulations of the present invention that areparticularly advantageous because they provide improved efficacy andtolerability in vivo, are serum-stable, are substantially non-toxic, arecapable of accessing extravascular sites, and are capable of reachingtarget cell populations.

The lipid particles and compositions of the present invention may beused for a variety of purposes, including the delivery of associated orencapsulated therapeutic agents to cells, both in vitro and in vivo.Accordingly, the present invention provides methods for treatingdiseases or disorders in a subject in need thereof, by contacting thesubject with a lipid particle described herein comprising one or moresuitable therapeutic agents.

Various exemplary embodiments of the lipid particles of the invention,as well as compositions and formulations comprising the same, and theiruse to deliver therapeutic agents and modulate target gene and proteinexpression, are described in further detail below.

II. Definitions

As used herein, the following terms have the meanings ascribed to themunless specified otherwise.

The term “interfering RNA” or “RNAi” or “interfering RNA sequence”refers to single-stranded RNA (e.g., mature miRNA) or double-strandedRNA (i.e., duplex RNA such as siRNA, aiRNA, or pre-miRNA) that iscapable of reducing or inhibiting the expression of a target gene orsequence (e.g., by mediating the degradation or inhibiting thetranslation of mRNAs which are complementary to the interfering RNAsequence) when the interfering RNA is in the same cell as the targetgene or sequence. Interfering RNA thus refers to the single-stranded RNAthat is complementary to a target mRNA sequence or to thedouble-stranded RNA formed by two complementary strands or by a single,self-complementary strand. Interfering RNA may have substantial orcomplete identity to the target gene or sequence, or may comprise aregion of mismatch (i.e., a mismatch motif). The sequence of theinterfering RNA can correspond to the full-length target gene, or asubsequence thereof.

Interfering RNA includes “small-interfering RNA” or “siRNA,” e.g.,interfering RNA of about 15-60, 15-50, or 15-40 (duplex) nucleotides inlength, more typically about 15-30, 15-25, or 19-25 (duplex) nucleotidesin length, and is preferably about 20-24, 21-22, or 21-23 (duplex)nucleotides in length (e.g., each complementary sequence of thedouble-stranded siRNA is 15-60, 15-50, 15-40, 15-30, 15-25, or 19-25nucleotides in length, preferably about 20-24, 21-22, or 21-23nucleotides in length, and the double-stranded siRNA is about 15-60,15-50, 15-40, 15-30, 15-25, or 19-25 base pairs in length, preferablyabout 18-22, 19-20, or 19-21 base pairs in length). siRNA duplexes maycomprise 3′ overhangs of about 1 to about 4 nucleotides or about 2 toabout 3 nucleotides and 5′ phosphate termini. Examples of siRNA include,without limitation, a double-stranded polynucleotide molecule assembledfrom two separate stranded molecules, wherein one strand is the sensestrand and the other is the complementary antisense strand; adouble-stranded polynucleotide molecule assembled from a single strandedmolecule, where the sense and antisense regions are linked by a nucleicacid-based or non-nucleic acid-based linker; a double-strandedpolynucleotide molecule with a hairpin secondary structure havingself-complementary sense and antisense regions; and a circularsingle-stranded polynucleotide molecule with two or more loop structuresand a stem having self-complementary sense and antisense regions, wherethe circular polynucleotide can be processed in vivo or in vitro togenerate an active double-stranded siRNA molecule.

Preferably, siRNA are chemically synthesized. siRNA can also begenerated by cleavage of longer dsRNA (e.g., dsRNA greater than about 25nucleotides in length) with the E. coli RNase III or Dicer. Theseenzymes process the dsRNA into biologically active siRNA (see, e.g.,Yang et al., Proc. Natl. Acad. Sci. USA, 99:9942-9947 (2002); Calegariet al., Proc. Natl. Acad. Sci. USA, 99:14236 (2002); Byrom et al.,Ambion TechNotes, 10(1):4-6 (2003); Kawasaki et al., Nucleic Acids Res.,31:981-987 (2003); Knight et al., Science, 293:2269-2271 (2001); andRobertson et al., J. Biol. Chem., 243:82 (1968)). Preferably, dsRNA areat least 50 nucleotides to about 100, 200, 300, 400, or 500 nucleotidesin length. A dsRNA may be as long as 1000, 1500, 2000, 5000 nucleotidesin length, or longer. The dsRNA can encode for an entire gene transcriptor a partial gene transcript. In certain instances, siRNA may be encodedby a plasmid (e.g., transcribed as sequences that automatically foldinto duplexes with hairpin loops).

As used herein, the term “mismatch motif” or “mismatch region” refers toa portion of an interfering RNA (e.g., siRNA, aiRNA, miRNA) sequencethat does not have 100% complementarity to its target sequence. Aninterfering RNA may have at least one, two, three, four, five, six, ormore mismatch regions. The mismatch regions may be contiguous or may beseparated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more nucleotides.The mismatch motifs or regions may comprise a single nucleotide or maycomprise two, three, four, five, or more nucleotides.

An “effective amount” or “therapeutically effective amount” of an activeagent or therapeutic agent such as an interfering RNA is an amountsufficient to produce the desired effect, e.g., an inhibition ofexpression of a target sequence in comparison to the normal expressionlevel detected in the absence of an interfering RNA. Inhibition ofexpression of a target gene or target sequence is achieved when thevalue obtained with an interfering RNA relative to the control is about90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%,20%, 15%, 10%, 5%, or 0%. Suitable assays for measuring expression of atarget gene or target sequence include, e.g., examination of protein orRNA levels using techniques known to those of skill in the art such asdot blots, northern blots, in situ hybridization, ELISA,immunoprecipitation, enzyme function, as well as phenotypic assays knownto those of skill in the art.

By “decrease,” “decreasing,” “reduce,” or “reducing” of an immuneresponse by an interfering RNA is intended to mean a detectable decreaseof an immune response to a given interfering RNA (e.g., a modifiedinterfering RNA). The amount of decrease of an immune response by amodified interfering RNA may be determined relative to the level of animmune response in the presence of an unmodified interfering RNA. Adetectable decrease can be about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, or morelower than the immune response detected in the presence of theunmodified interfering RNA. A decrease in the immune response tointerfering RNA is typically measured by a decrease in cytokineproduction (e.g., IFNγ, IFNα, TNFα, IL-6, or IL-12) by a responder cellin vitro or a decrease in cytokine production in the sera of a mammaliansubject after administration of the interfering RNA.

As used herein, the term “responder cell” refers to a cell, preferably amammalian cell, that produces a detectable immune response whencontacted with an immunostimulatory interfering RNA such as anunmodified siRNA. Exemplary responder cells include, e.g., dendriticcells, macrophages, peripheral blood mononuclear cells (PBMCs),splenocytes, and the like. Detectable immune responses include, e.g.,production of cytokines or growth factors such as TNF-α, IFN-α, IFN-β,IFN-γ, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-10, IL-12, IL-13, TGF, andcombinations thereof.

“Substantial identity” refers to a sequence that hybridizes to areference sequence under stringent conditions, or to a sequence that hasa specified percent identity over a specified region of a referencesequence.

The phrase “stringent hybridization conditions” refers to conditionsunder which a nucleic acid will hybridize to its target sequence,typically in a complex mixture of nucleic acids, but to no othersequences. Stringent conditions are sequence-dependent and will bedifferent in different circumstances. Longer sequences hybridizespecifically at higher temperatures. An extensive guide to thehybridization of nucleic acids is found in Tijssen, Techniques inBiochemistry and Molecular Biology—Hybridization with Nucleic Probes,“Overview of principles of hybridization and the strategy of nucleicacid assays” (1993). Generally, stringent conditions are selected to beabout 5-10° C. lower than the thermal melting point (T_(m)) for thespecific sequence at a defined ionic strength pH. The T_(m) is thetemperature (under defined ionic strength, pH, and nucleicconcentration) at which 50% of the probes complementary to the targethybridize to the target sequence at equilibrium (as the target sequencesare present in excess, at T_(m), 50% of the probes are occupied atequilibrium). Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide. For selective orspecific hybridization, a positive signal is at least two timesbackground, preferably 10 times background hybridization.

Exemplary stringent hybridization conditions can be as follows: 50%formamide, 5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS,incubating at 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C. ForPCR, a temperature of about 36° C. is typical for low stringencyamplification, although annealing temperatures may vary between about32° C. and 48° C. depending on primer length. For high stringency PCRamplification, a temperature of about 62° C. is typical, although highstringency annealing temperatures can range from about 50° C. to about65° C., depending on the primer length and specificity. Typical cycleconditions for both high and low stringency amplifications include adenaturation phase of 90° C.-95° C. for 30 sec.-2 min., an annealingphase lasting 30 sec.-2 min., and an extension phase of about 72° C. for1-2 min. Protocols and guidelines for low and high stringencyamplification reactions are provided, e.g., in Innis et al., PCRProtocols, A Guide to Methods and Applications, Academic Press, Inc.N.Y. (1990).

Nucleic acids that do not hybridize to each other under stringentconditions are still substantially identical if the polypeptides whichthey encode are substantially identical. This occurs, for example, whena copy of a nucleic acid is created using the maximum codon degeneracypermitted by the genetic code. In such cases, the nucleic acidstypically hybridize under moderately stringent hybridization conditions.Exemplary “moderately stringent hybridization conditions” include ahybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C.,and a wash in 1×SSC at 45° C. A positive hybridization is at least twicebackground. Those of ordinary skill will readily recognize thatalternative hybridization and wash conditions can be utilized to provideconditions of similar stringency. Additional guidelines for determininghybridization parameters are provided in numerous references, e.g.,Current Protocols in Molecular Biology, Ausubel et al., eds.

The terms “substantially identical” or “substantial identity,” in thecontext of two or more nucleic acids, refer to two or more sequences orsubsequences that are the same or have a specified percentage ofnucleotides that are the same (i.e., at least about 60%, preferably atleast about 65%, 70%, 75%, 80%, 85%, 90%, or 95% identity over aspecified region), when compared and aligned for maximum correspondenceover a comparison window, or designated region as measured using one ofthe following sequence comparison algorithms or by manual alignment andvisual inspection. This definition, when the context indicates, alsorefers analogously to the complement of a sequence. Preferably, thesubstantial identity exists over a region that is at least about 5, 10,15, 20, 25, 30, 35, 40, 45, 50, 55, or 60 nucleotides in length.

For sequence comparison, typically one sequence acts as a referencesequence, to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are entered into acomputer, subsequence coordinates are designated, if necessary, andsequence algorithm program parameters are designated. Default programparameters can be used, or alternative parameters can be designated. Thesequence comparison algorithm then calculates the percent sequenceidentities for the test sequences relative to the reference sequence,based on the program parameters.

A “comparison window,” as used herein, includes reference to a segmentof any one of a number of contiguous positions selected from the groupconsisting of from about 5 to about 60, usually about 10 to about 45,more usually about 15 to about 30, in which a sequence may be comparedto a reference sequence of the same number of contiguous positions afterthe two sequences are optimally aligned. Methods of alignment ofsequences for comparison are well known in the art. Optimal alignment ofsequences for comparison can be conducted, e.g., by the local homologyalgorithm of Smith and Waterman, Adv. Appl. Math., 2:482 (1981), by thehomology alignment algorithm of Needleman and Wunsch, J. Mol. Biol.,48:443 (1970), by the search for similarity method of Pearson andLipman, Proc. Natl. Acad. Sci. USA, 85:2444 (1988), by computerizedimplementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA inthe Wisconsin Genetics Software Package, Genetics Computer Group, 575Science Dr., Madison, Wis.), or by manual alignment and visualinspection (see, e.g., Current Protocols in Molecular Biology, Ausubelet al., eds. (1995 supplement)).

A preferred example of algorithms that are suitable for determiningpercent sequence identity and sequence similarity are the BLAST andBLAST 2.0 algorithms, which are described in Altschul et al., Nuc. AcidsRes., 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol.,215:403-410 (1990), respectively. BLAST and BLAST 2.0 are used, with theparameters described herein, to determine percent sequence identity forthe nucleic acids of the invention. Software for performing BLASTanalyses is publicly available through the National Center forBiotechnology Information (http://www.ncbi.nlm.nih.gov/).

The BLAST algorithm also performs a statistical analysis of thesimilarity between two sequences (see, e.g., Karlin and Altschul, Proc.Natl. Acad. Sci. USA, 90:5873-5787 (1993)). One measure of similarityprovided by the BLAST algorithm is the smallest sum probability (P(N)),which provides an indication of the probability by which a match betweentwo nucleotide sequences would occur by chance. For example, a nucleicacid is considered similar to a reference sequence if the smallest sumprobability in a comparison of the test nucleic acid to the referencenucleic acid is less than about 0.2, more preferably less than about0.01, and most preferably less than about 0.001.

The term “nucleic acid” as used herein refers to a polymer containing atleast two deoxyribonucleotides or ribonucleotides in either single- ordouble-stranded form and includes DNA and RNA. DNA may be in the formof, e.g., antisense molecules, plasmid DNA, pre-condensed DNA, a PCRproduct, vectors (P1, PAC, BAC, YAC, artificial chromosomes), expressioncassettes, chimeric sequences, chromosomal DNA, or derivatives andcombinations of these groups. RNA may be in the form of siRNA,asymmetrical interfering RNA (aiRNA), microRNA (miRNA), mRNA, tRNA,rRNA, tRNA, viral RNA (vRNA), and combinations thereof. Nucleic acidsinclude nucleic acids containing known nucleotide analogs or modifiedbackbone residues or linkages, which are synthetic, naturally occurring,and non-naturally occurring, and which have similar binding propertiesas the reference nucleic acid. Examples of such analogs include, withoutlimitation, phosphorothioates, phosphoramidates, methyl phosphonates,chiral-methyl phosphonates, 2′-O-methyl ribonucleotides, andpeptide-nucleic acids (PNAs). Unless specifically limited, the termencompasses nucleic acids containing known analogues of naturalnucleotides that have similar binding properties as the referencenucleic acid. Unless otherwise indicated, a particular nucleic acidsequence also implicitly encompasses conservatively modified variantsthereof (e.g., degenerate codon substitutions), alleles, orthologs,SNPs, and complementary sequences as well as the sequence explicitlyindicated. Specifically, degenerate codon substitutions may be achievedby generating sequences in which the third position of one or moreselected (or all) codons is substituted with mixed-base and/ordeoxyinosine residues (Batzer et al., Nucleic Acid Res., 19:5081 (1991);Ohtsuka et al., J. Biol. Chem., 260:2605-2608 (1985); Rossolini et al.,Mol. Cell. Probes, 8:91-98 (1994)). “Nucleotides” contain a sugardeoxyribose (DNA) or ribose (RNA), a base, and a phosphate group.Nucleotides are linked together through the phosphate groups. “Bases”include purines and pyrimidines, which further include natural compoundsadenine, thymine, guanine, cytosine, uracil, inosine, and naturalanalogs, and synthetic derivatives of purines and pyrimidines, whichinclude, but are not limited to, modifications which place new reactivegroups such as, but not limited to, amines, alcohols, thiols,carboxylates, and alkylhalides.

The term “gene” refers to a nucleic acid (e.g., DNA or RNA) sequencethat comprises partial length or entire length coding sequencesnecessary for the production of a polypeptide or precursor polypeptide.

“Gene product,” as used herein, refers to a product of a gene such as anRNA transcript or a polypeptide.

The term “lipid” refers to a group of organic compounds that include,but are not limited to, esters of fatty acids and are characterized bybeing insoluble in water, but soluble in many organic solvents. They areusually divided into at least three classes: (1) “simple lipids,” whichinclude fats and oils as well as waxes; (2) “compound lipids,” whichinclude phospholipids and glycolipids; and (3) “derived lipids” such assteroids.

A “lipid particle” is used herein to refer to a lipid formulation thatcan be used to deliver an active agent or therapeutic agent, such as anucleic acid (e.g., an interfering RNA), to a target site of interest.In the lipid particle of the invention, which is typically formed from acationic lipid, a non-cationic lipid, and a conjugated lipid thatprevents aggregation of the particle, the active agent or therapeuticagent may be encapsulated in the lipid, thereby protecting the agentfrom enzymatic degradation.

As used herein, the term “SNALP” refers to a stable nucleic acid-lipidparticle. A SNALP represents a particle made from lipids (e.g., acationic lipid, a non-cationic lipid, and a conjugated lipid thatprevents aggregation of the particle), wherein the nucleic acid (e.g.,siRNA, aiRNA, miRNA, ssDNA, dsDNA, ssRNA, short hairpin RNA (shRNA),dsRNA, or a plasmid, including plasmids from which an interfering RNA istranscribed) is fully encapsulated within the lipid. As used herein, theterm “SNALP” includes an SPLP, which is the term used to refer to anucleic acid-lipid particle comprising a nucleic acid (e.g., a plasmid)encapsulated within the lipid. SNALP and SPLP typically contain acationic lipid, a non-cationic lipid, and a lipid conjugate (e.g., aPEG-lipid conjugate). SNALP and SPLP are extremely useful for systemicapplications, as they can exhibit extended circulation lifetimesfollowing intravenous (i.v.) injection, they can accumulate at distalsites (e.g., sites physically separated from the administration site),and they can mediate expression of the transfected gene or silencing oftarget gene expression at these distal sites. SPLP include “pSPLP,”which comprise an encapsulated condensing agent-nucleic acid complex asset forth in PCT Publication No. WO 00/03683, the disclosure of which isherein incorporated by reference in its entirety for all purposes.

The lipid particles of the invention (e.g., SNALP) typically have a meandiameter of from about 40 nm to about 150 nm, from about 50 nm to about150 nm, from about 60 nm to about 130 nm, from about 70 nm to about 110nm, or from about 70 to about 90 nm, and are substantially non-toxic. Inaddition, nucleic acids, when present in the lipid particles of theinvention, are resistant in aqueous solution to degradation with anuclease. Nucleic acid-lipid particles and their method of preparationare disclosed in, e.g., U.S. Patent Publication Nos. 20040142025 and20070042031, the disclosures of which are herein incorporated byreference in their entirety for all purposes.

As used herein, “lipid encapsulated” can refer to a lipid particle thatprovides an active agent or therapeutic agent, such as a nucleic acid(e.g., an interfering RNA), with full encapsulation, partialencapsulation, or both. In a preferred embodiment, the nucleic acid isfully encapsulated in the lipid particle (e.g., to form an SPLP, pSPLP,SNALP, or other nucleic acid-lipid particle).

The term “lipid conjugate” refers to a conjugated lipid that inhibitsaggregation of lipid particles. Such lipid conjugates include, but arenot limited to, polyamide oligomers (e.g., ATTA-lipid conjugates),PEG-lipid conjugates, such as PEG coupled to dialkyloxypropyls, PEGcoupled to diacylglycerols, PEG coupled to cholesterol, PEG coupled tophosphatidylethanolamines, PEG conjugated to ceramides (see, e.g., U.S.Pat. No. 5,885,613, the disclosure of which is herein incorporated byreference in its entirety for all purposes), cationic PEG lipids, andmixtures thereof. PEG can be conjugated directly to the lipid or may belinked to the lipid via a linker moiety. Any linker moiety suitable forcoupling the PEG to a lipid can be used including, e.g., non-estercontaining linker moieties and ester-containing linker moieties. Inpreferred embodiments, non-ester containing linker moieties are used.

The term “amphipathic lipid” refers, in part, to any suitable materialwherein the hydrophobic portion of the lipid material orients into ahydrophobic phase, while the hydrophilic portion orients toward theaqueous phase. Hydrophilic characteristics derive from the presence ofpolar or charged groups such as carbohydrates, phosphate, carboxylic,sulfato, amino, sulfhydryl, nitro, hydroxyl, and other like groups.Hydrophobicity can be conferred by the inclusion of apolar groups thatinclude, but are not limited to, long-chain saturated and unsaturatedaliphatic hydrocarbon groups and such groups substituted by one or morearomatic, cycloaliphatic, or heterocyclic group(s). Examples ofamphipathic compounds include, but are not limited to, phospholipids,aminolipids, and sphingolipids.

Representative examples of phospholipids include, but are not limitedto, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine,phosphatidylinositol, phosphatidic acid, palmitoyloleoylphosphatidylcholine, lysophosphatidylcholine,lysophosphatidylethanolamine, dipalmitoylphosphatidylcholine,dioleoylphosphatidylcholine, distearoylphosphatidylcholine, anddilinoleoylphosphatidylcholine. Other compounds lacking in phosphorus,such as sphingolipid, glycosphingolipid families, diacylglycerols, andβ-acyloxyacids, are also within the group designated as amphipathiclipids. Additionally, the amphipathic lipids described above can bemixed with other lipids including triglycerides and sterols.

The term “neutral lipid” refers to any of a number of lipid species thatexist either in an uncharged or neutral zwitterionic form at a selectedpH. At physiological pH, such lipids include, for example,diacylphosphatidylcholine, diacylphosphatidylethanolamine, ceramide,sphingomyelin, cephalin, cholesterol, cerebrosides, and diacylglycerols.

The term “non-cationic lipid” refers to any amphipathic lipid as well asany other neutral lipid or anionic lipid.

The term “anionic lipid” refers to any lipid that is negatively chargedat physiological pH. These lipids include, but are not limited to,phosphatidylglycerols, cardiolipins, diacylphosphatidylserines,diacylphosphatidic acids, N-dodecanoyl phosphatidylethanolamines,N-succinyl phosphatidylethanolamines,N-glutarylphosphatidylethanolamines, lysylphosphatidylglycerols,palmitoyloleyolphosphatidylglycerol (POPG), and other anionic modifyinggroups joined to neutral lipids.

The term “cationic lipid” refers to any of a number of lipid speciesthat carry a net positive charge at a selected pH, such as physiologicalpH (e.g., pH of about 7.0). It has been surprisingly found that cationiclipids comprising alkyl chains with multiple sites of unsaturation,e.g., at least two or three sites of unsaturation, are particularlyuseful for forming lipid particles with increased membrane fluidity. Anumber of cationic lipids and related analogs, which are also useful inthe present invention, have been described in U.S. Patent PublicationNos. 20060083780 and 20060240554; U.S. Pat. Nos. 5,208,036; 5,264,618;5,279,833; 5,283,185; 5,753,613; and 5,785,992; and PCT Publication No.WO 96/10390, the disclosures of which are herein incorporated byreference in their entirety for all purposes. Non-limiting examples ofcationic lipids are described in detail herein. In some cases, thecationic lipids comprise a protonatable tertiary amine (e.g., pHtitratable) head group, C18 alkyl chains, ether linkages between thehead group and alkyl chains, and 0 to 3 double bonds. Such lipidsinclude, e.g., DSDMA, DLinDMA, DLenDMA, and DODMA.

The term “hydrophobic lipid” refers to compounds having apolar groupsthat include, but are not limited to, long-chain saturated andunsaturated aliphatic hydrocarbon groups and such groups optionallysubstituted by one or more aromatic, cycloaliphatic, or heterocyclicgroup(s). Suitable examples include, but are not limited to,diacylglycerol, dialkylglycerol, N—N-dialkylamino,1,2-diacyloxy-3-aminopropane, and 1,2-dialkyl-3-aminopropane.

The term “fusogenic” refers to the ability of a lipid particle, such asa SNALP, to fuse with the membranes of a cell. The membranes can beeither the plasma membrane or membranes surrounding organelles, e.g.,endosome, nucleus, etc.

As used herein, the term “aqueous solution” refers to a compositioncomprising in whole, or in part, water.

As used herein, the term “organic lipid solution” refers to acomposition comprising in whole, or in part, an organic solvent having alipid.

“Distal site,” as used herein, refers to a physically separated site,which is not limited to an adjacent capillary bed, but includes sitesbroadly distributed throughout an organism.

“Serum-stable” in relation to nucleic acid-lipid particles such as SNALPmeans that the particle is not significantly degraded after exposure toa serum or nuclease assay that would significantly degrade free DNA orRNA. Suitable assays include, for example, a standard serum assay, aDNAse assay, or an RNAse assay.

“Systemic delivery,” as used herein, refers to delivery of lipidparticles that leads to a broad biodistribution of an active agent ortherapeutic agent such as an interfering RNA within an organism. Sometechniques of administration can lead to the systemic delivery ofcertain agents, but not others. Systemic delivery means that a useful,preferably therapeutic, amount of an agent is exposed to most parts ofthe body. To obtain broad biodistribution generally requires a bloodlifetime such that the agent is not rapidly degraded or cleared (such asby first pass organs (liver, lung, etc.) or by rapid, nonspecific cellbinding) before reaching a disease site distal to the site ofadministration. Systemic delivery of lipid particles can be by any meansknown in the art including, for example, intravenous, subcutaneous, andintraperitoneal. In a preferred embodiment, systemic delivery of lipidparticles is by intravenous delivery.

“Local delivery,” as used herein, refers to delivery of an active agentor therapeutic agent such as an interfering RNA directly to a targetsite within an organism. For example, an agent can be locally deliveredby direct injection into a disease site such as a tumor or other targetsite such as a site of inflammation or a target organ such as the liver,heart, pancreas, kidney, and the like.

The term “mammal” refers to any mammalian species such as a human,mouse, rat, dog, cat, hamster, guinea pig, rabbit, livestock, and thelike.

The term “cancer” refers to any member of a class of diseasescharacterized by the uncontrolled growth of aberrant cells. The termincludes all known cancers and neoplastic conditions, whethercharacterized as malignant, benign, soft tissue, or solid, and cancersof all stages and grades including pre- and post-metastatic cancers.Examples of different types of cancer include, but are not limited to,lung cancer, colon cancer, rectal cancer, anal cancer, bile duct cancer,small intestine cancer, stomach (gastric) cancer, esophageal cancer;gallbladder cancer, liver cancer, pancreatic cancer, appendix cancer,breast cancer, ovarian cancer; cervical cancer, prostate cancer, renalcancer (e.g., renal cell carcinoma), cancer of the central nervoussystem, glioblastoma, skin cancer, lymphomas, choriocarcinomas, head andneck cancers, osteogenic sarcomas, and blood cancers. Non-limitingexamples of specific types of liver cancer include hepatocellularcarcinoma (HCC), secondary liver cancer (e.g., caused by metastasis ofsome other non-liver cancer cell type), and hepatoblastoma. As usedherein, a “tumor” comprises one or more cancerous cells.

III. Description of the Embodiments

The present invention provides novel, serum-stable lipid particlescomprising one or more active agents or therapeutic agents, methods ofmaking the lipid particles, and methods of delivering and/oradministering the lipid particles (e.g., for the treatment of a diseaseor disorder).

In one aspect, the present invention provides lipid particlescomprising: (a) one or more active agents or therapeutic agents; (b) oneor more cationic lipids comprising from about 50 mol % to about 85 mol %of the total lipid present in the particle; (c) one or more non-cationiclipids comprising from about 13 mol % to about 49.5 mol % of the totallipid present in the particle; and (d) one or more conjugated lipidsthat inhibit aggregation of particles comprising from about 0.5 mol % toabout 2 mol % of the total lipid present in the particle.

In certain embodiments, the active agent or therapeutic agent is fullyencapsulated within the lipid portion of the lipid particle such thatthe active agent or therapeutic agent in the lipid particle is resistantin aqueous solution to enzymatic degradation, e.g., by a nuclease orprotease. In certain other embodiments, the lipid particles aresubstantially non-toxic to mammals such as humans.

In some embodiments, the active agent or therapeutic agent comprises anucleic acid. In certain instances, the nucleic acid comprises aninterfering RNA molecule such as, e.g., an siRNA, aiRNA, miRNA, ormixtures thereof. In certain other instances, the nucleic acid comprisessingle-stranded or double-stranded DNA, RNA, or a DNA/RNA hybrid suchas, e.g., an antisense oligonucleotide, a ribozyme, a plasmid, animmunostimulatory oligonucleotide, or mixtures thereof.

In other embodiments, the active agent or therapeutic agent comprises apeptide or polypeptide. In certain instances, the peptide or polypeptidecomprises an antibody such as, e.g., a polyclonal antibody, a monoclonalantibody, an antibody fragment; a humanized antibody, a recombinantantibody, a recombinant human antibody, a Primatized™ antibody, ormixtures thereof. In certain other instances, the peptide or polypeptidecomprises a cytokine, a growth factor, an apoptotic factor, adifferentiation-inducing factor, a cell-surface receptor, a ligand, ahormone, a small molecule (e.g., small organic molecule or compound), ormixtures thereof.

In preferred embodiments, the active agent or therapeutic agentcomprises an siRNA. In one embodiment, the siRNA molecule comprises adouble-stranded region of about 15 to about 60 nucleotides in length(e.g., about 15-60, 15-50, 15-40, 15-30, 15-25, or 19-25 nucleotides inlength, or 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides inlength). The siRNA molecules of the invention are capable of silencingthe expression of a target sequence in vitro and/or in vivo.

In some embodiments, the siRNA molecule comprises at least one modifiednucleotide. In certain preferred embodiments, the siRNA moleculecomprises one, two, three, four, five, six, seven, eight, nine, ten, ormore modified nucleotides in the double-stranded region. In certaininstances, the siRNA comprises from about 1% to about 100% (e.g., about1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, 95%, or 100%) modified nucleotides in thedouble-stranded region. In preferred embodiments, less than about 25%(e.g., less than about 25%, 20%, 15%, 10%, or 5%) or from about 1% toabout 25% (e.g., from about 1%-25%, 5%-25%, 10%-25%, 15%-25%, 20%-25%,or 10%-20%) of the nucleotides in the double-stranded region comprisemodified nucleotides.

In other embodiments, the siRNA molecule comprises modified nucleotidesincluding, but not limited to, 2′-O-methyl (2′OMe) nucleotides,2′-deoxy-2′-fluoro (2′F) nucleotides, 2′-deoxy nucleotides,2′-O-(2-methoxyethyl) (MOE) nucleotides, locked nucleic acid (LNA)nucleotides, and mixtures thereof. In preferred embodiments, the siRNAcomprises 2′OMe nucleotides (e.g., 2′OMe purine and/or pyrimidinenucleotides) such as, for example, 2′OMe-guanosine nucleotides,2′OMe-uridine nucleotides, 2′OMe-adenosine nucleotides, 2′OMe-cytosinenucleotides, and mixtures thereof. In certain instances, the siRNA doesnot comprise 2′OMe-cytosine nucleotides. In other embodiments, the siRNAcomprises a hairpin loop structure.

The siRNA may comprise modified nucleotides in one strand (i.e., senseor antisense) or both strands of the double-stranded region of the siRNAmolecule. Preferably, uridine and/or guanosine nucleotides are modifiedat selective positions in the double-stranded region of the siRNAduplex. With regard to uridine nucleotide modifications, at least one,two, three, four, five, six, or more of the uridine nucleotides in thesense and/or antisense strand can be a modified uridine nucleotide suchas a 2′OMe-uridine nucleotide. In some embodiments, every uridinenucleotide in the sense and/or antisense strand is a 2′OMe-uridinenucleotide. With regard to guanosine nucleotide modifications, at leastone, two, three, four, five, six, or more of the guanosine nucleotidesin the sense and/or antisense strand can be a modified guanosinenucleotide such as a 2′OMe-guanosine nucleotide. In some embodiments,every guanosine nucleotide in the sense and/or antisense strand is a2′OMe-guanosine nucleotide.

In certain embodiments, at least one, two, three, four, five, six,seven, or more 5′-GU-3′ motifs in an siRNA sequence may be modified,e.g., by introducing mismatches to eliminate the 5′-GU-3′ motifs and/orby introducing modified nucleotides such as 2′OMe nucleotides. The5′-GU-3′ motif can be in the sense strand, the antisense strand, or bothstrands of the siRNA sequence. The 5′-GU-3′ motifs may be adjacent toeach other or, alternatively, they may be separated by 1, 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, or more nucleotides.

In some preferred embodiments, a modified siRNA molecule is lessimmunostimulatory than a corresponding unmodified siRNA sequence. Insuch embodiments, the modified siRNA molecule with reducedimmunostimulatory properties advantageously retains RNAi activityagainst the target sequence. In another embodiment, theimmunostimulatory properties of the modified siRNA molecule and itsability to silence target gene expression can be balanced or optimizedby the introduction of minimal and selective 2′OMe modifications withinthe siRNA sequence such as, e.g., within the double-stranded region ofthe siRNA duplex. In certain instances, the modified siRNA is at leastabout 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or100% less immunostimulatory than the corresponding unmodified siRNA. Itwill be readily apparent to those of skill in the art that theimmunostimulatory properties of the modified siRNA molecule and thecorresponding unmodified siRNA molecule can be determined by, forexample, measuring INF-α and/or IL-6 levels from about two to abouttwelve hours after systemic administration in a mammal or transfectionof a mammalian responder cell using an appropriate lipid-based deliverysystem (such as the SNALP delivery system disclosed herein).

In certain embodiments, a modified siRNA molecule has an IC₅₀ (i.e.,half-maximal inhibitory concentration) less than or equal to ten-foldthat of the corresponding unmodified siRNA (i.e., the modified siRNA hasan IC₅₀ that is less than or equal to ten-times the IC₅₀ of thecorresponding unmodified siRNA). In other embodiments, the modifiedsiRNA has an IC₅₀ less than or equal to three-fold that of thecorresponding unmodified siRNA sequence. In yet other embodiments, themodified siRNA has an IC₅₀ less than or equal to two-fold that of thecorresponding unmodified siRNA. It will be readily apparent to those ofskill in the art that a dose-response curve can be generated and theIC₅₀ values for the modified siRNA and the corresponding unmodifiedsiRNA can be readily determined using methods known to those of skill inthe art.

In yet another embodiment, a modified siRNA molecule is capable ofsilencing at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% of theexpression of the target sequence relative to the correspondingunmodified siRNA sequence.

In some embodiments, the siRNA molecule does not comprise phosphatebackbone modifications, e.g., in the sense and/or antisense strand ofthe double-stranded region. In other embodiments, the siRNA comprisesone, two, three, four, or more phosphate backbone modifications, e.g.,in the sense and/or antisense strand of the double-stranded region. Inpreferred embodiments, the siRNA does not comprise phosphate backbonemodifications.

In further embodiments, the siRNA does not comprise 2′-deoxynucleotides, e.g., in the sense and/or antisense strand of thedouble-stranded region. In yet further embodiments, the siRNA comprisesone, two, three, four, or more 2′-deoxy nucleotides, e.g., in the senseand/or antisense strand of the double-stranded region. In preferredembodiments, the siRNA does not comprise 2′-deoxy nucleotides.

In certain instances, the nucleotide at the 3′-end of thedouble-stranded region in the sense and/or antisense strand is not amodified nucleotide. In certain other instances, the nucleotides nearthe 3′-end (e.g., within one, two, three, or four nucleotides of the3′-end) of the double-stranded region in the sense and/or antisensestrand are not modified nucleotides.

The siRNA molecules described herein may have 3′ overhangs of one, two,three, four, or more nucleotides on one or both sides of thedouble-stranded region, or may lack overhangs (i.e., have blunt ends) onone or both sides of the double-stranded region. Preferably, the siRNAhas 3′ overhangs of two nucleotides on each side of the double-strandedregion. In certain instances, the 3′ overhang on the antisense strandhas complementarity to the target sequence and the 3′ overhang on thesense strand has complementarity to a complementary strand of the targetsequence. Alternatively, the 3′ overhangs do not have complementarity tothe target sequence or the complementary strand thereof. In someembodiments, the 3′ overhangs comprise one, two, three, four, or morenucleotides such as 2′-deoxy (2′H) nucleotides. In certain preferredembodiments, the 3′ overhangs comprise deoxythymidine (dT) and/oruridine nucleotides. In other embodiments, one or more of thenucleotides in the 3′ overhangs on one or both sides of thedouble-stranded region comprise modified nucleotides. Non-limitingexamples of modified nucleotides are described above and include 2′OMenucleotides, 2′-deoxy-2′F nucleotides, 2′-deoxy nucleotides, 2′-O-2-MOEnucleotides, LNA nucleotides, and mixtures thereof. In preferredembodiments, one, two, three, four, or more nucleotides in the 3′overhangs present on the sense and/or antisense strand of the siRNAcomprise 2′OMe nucleotides (e.g., 2′OMe purine and/or pyrimidinenucleotides) such as, for example, 2′OMe-guanosine nucleotides,2′OMe-uridine nucleotides, 2′OMe-adenosine nucleotides, 2′OMe-cytosinenucleotides, and mixtures thereof.

The siRNA may comprise at least one or a cocktail (e.g., at least two,three, four, five, six, seven, eight, nine, ten, or more) of unmodifiedand/or modified siRNA sequences that silence target gene expression. Thecocktail of siRNA may comprise sequences which are directed to the sameregion or domain (e.g., a “hot spot”) and/or to different regions ordomains of one or more target genes. In certain instances, one or more(e.g., at least two, three, four, five, six, seven, eight, nine, ten, ormore) modified siRNA that silence target gene expression are present ina cocktail. In certain other instances, one or more (e.g., at least two,three, four, five, six, seven, eight, nine, ten, or more) unmodifiedsiRNA sequences that silence target gene expression are present in acocktail.

In some embodiments, the antisense strand of the siRNA moleculecomprises or consists of a sequence that is at least about 80%, 85%,90%, 95%, 96%, 97%, 98%, or 99% complementary to the target sequence ora portion thereof. In other embodiments, the antisense strand of thesiRNA molecule comprises or consists of a sequence that is 100%complementary to the target sequence or a portion thereof. In furtherembodiments, the antisense strand of the siRNA molecule comprises orconsists of a sequence that specifically hybridizes to the targetsequence or a portion thereof.

In further embodiments, the sense strand of the siRNA molecule comprisesor consists of a sequence that is at least about 80%, 85%, 90%, 95%,96%, 97%, 98%, or 99% identical to the target sequence or a portionthereof. In additional embodiments, the sense strand of the siRNAmolecule comprises or consists of a sequence that is 100% identical tothe target sequence or a portion thereof.

In the lipid particles of the invention (e.g., SNALP comprising aninterfering RNA such as siRNA), the cationic lipid may comprise, e.g.,one or more of the following: 1,2-dilinoleyloxy-N,N-dimethylaminopropane(DLinDMA), 1,2-dilinolenyloxy-N,N-dimethylaminopropane (DLenDMA),2,2-dilinoleyl-4-(2-dimethylaminoethyl)-[1,3]-dioxolane (DLin-K-C2-DMA;“XTC2”), 2,2-dilinoleyl-4-(3-dimethylaminopropyl)-[1,3]-dioxolane(DLin-K-C3-DMA), 2,2-dilinoleyl-4-(4-dimethylaminobutyl)-[1,3]-dioxolane(DLin-K-C4-DMA), 2,2-dilinoleyl-5-dimethylaminomethyl-[1,3]-dioxane(DLin-K6-DMA), 2,2-dilinoleyl-4-N-methylpepiazino-[1,3]-dioxolane(DLin-K-MPZ), 2,2-dilinoleyl-4-dimethylaminomethyl-[1,3]-dioxolane(DLin-K-DMA), 1,2-dilinoleylcarbamoyloxy-3-dimethylaminopropane(DLin-C-DAP), 1,2-dilinoleyoxy-3-(dimethylamino)acetoxypropane(DLin-DAC), 1,2-dilinoleyoxy-3-morpholinopropane (DLin-MA),1,2-dilinoleoyl-3-dimethylaminopropane (DLinDAP),1,2-dilinoleylthio-3-dimethylaminopropane (DLin-S-DMA),1-linoleoyl-2-linoleyloxy-3-dimethylaminopropane (DLin-2-DMAP),1,2-dilinoleyloxy-3-trimethylaminopropane chloride salt (DLin-TMA.Cl),1,2-dilinoleoyl-3-trimethylaminopropane chloride salt (DLin-TAP.Cl),1,2-dilinoleyloxy-3-(N-methylpiperazino)propane (DLin-MPZ),3-(N,N-dilinoleylamino)-1,2-propanediol (DLinAP),3-(N,N-dioleylamino)-1,2-propanedio (DOAP),1,2-dilinoleyloxo-3-(2-N,N-dimethylamino)ethoxypropane (DLin-EG-DMA),N,N-dioleyl-N,N-dimethylammonium chloride (DODAC),1,2-dioleyloxy-N,N-dimethylaminopropane (DODMA),1,2-distearyloxy-N,N-dimethylaminopropane (DSDMA),N-(1-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA),N,N-distearyl-N,N-dimethylammonium bromide (DDAB),N-(1-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP),3-(N—(N′,N′-dimethylaminoethane)-carbamoyl)cholesterol (DC-Chol),N-(1,2-dimyristyloxyprop-3-yl)-N,N-dimethyl-N-hydroxyethyl ammoniumbromide (DMRIE),2,3-dioleyloxy-N-[2(spermine-carboxamido)ethyl]-N,N-dimethyl-1-propanaminiumtrifluoroacetate(DOSPA), dioctadecylamidoglycyl spermine (DOGS),3-dimethylamino-2-(cholest-5-en-3-beta-oxybutan-4-oxy)-1-(cis,cis-9,12-octadecadienoxy)propane(CLinDMA),2-[5′-(cholest-5-en-3-beta-oxy)-3′-oxapentoxy)-3-dimethyl-1-(cis,cis-9′,1-2′-octadecadienoxy)propane(CpLinDMA), N,N-dimethyl-3,4-dioleyloxybenzylamine (DMOBA),1,2-N,N′-dioleylcarbamyl-3-dimethylaminopropane (DOcarbDAP),1,2-N,N′-dilinoleylcarbamyl-3-dimethylaminopropane (DLincarbDAP), ormixtures thereof. In certain preferred embodiments, the cationic lipidis DLinDMA, DLin-K-C2-DMA (“XTC2”), or mixtures thereof.

The synthesis of cationic lipids such as DLin-K-C2-DMA (“XTC2”),DLin-K-C3-DMA, DLin-K-C4-DMA, DLin-K6-DMA, and DLin-K-MPZ, as well asadditional cationic lipids, is described in U.S. Provisional ApplicationNo. 61/104,212, filed Oct. 9, 2008, the disclosure of which is hereinincorporated by reference in its entirety for all purposes. Thesynthesis of cationic lipids such as DLin-K-DMA, DLin-C-DAP, DLin-DAC,DLin-MA, DLinDAP, DLin-S-DMA, DLin-2-DMAP, DLin-TMA.Cl, DLin-TAP.Cl,DLin-MPZ, DLinAP, DOAP, and DLin-EG-DMA, as well as additional cationiclipids, is described in PCT Application No. PCT/US08/88676, filed Dec.31, 2008, the disclosure of which is herein incorporated by reference inits entirety for all purposes. The synthesis of cationic lipids such asCLinDMA, as well as additional cationic lipids, is described in U.S.Patent Publication No. 20060240554, the disclosure of which is hereinincorporated by reference in its entirety for all purposes.

In some embodiments, the cationic lipid may comprise from about 50 mol %to about 90 mol %, from about 50 mol % to about 85 mol %, from about 50mol % to about 80 mol %, from about 50 mol % to about 75 mol %, fromabout 50 mol % to about 70 mol %, from about 50 mol % to about 65 mol %,or from about 50 mol % to about 60 mol % of the total lipid present inthe particle.

In other embodiments, the cationic lipid may comprise from about 55 mol% to about 90 mol %, from about 55 mol % to about 85 mol %, from about55 mol % to about 80 mol %, from about 55 mol % to about 75 mol %, fromabout 55 mol % to about 70 mol %, or from about 55 mol % to about 65 mol% of the total lipid present in the particle.

In yet other embodiments, the cationic lipid may comprise from about 60mol % to about 90 mol %, from about 60 mol % to about 85 mol %, fromabout 60 mol % to about 80 mol %, from about 60 mol % to about 75 mol %,or from about 60 mol % to about 70 mol % of the total lipid present inthe particle.

In still yet other embodiments, the cationic lipid may comprise fromabout 65 mol % to about 90 mol %, from about 65 mol % to about 85 mol %,from about 65 mol % to about 80 mol %, or from about 65 mol % to about75 mol % of the total lipid present in the particle.

In further embodiments, the cationic lipid may comprise from about 70mol % to about 90 mol %, from about 70 mol % to about 85 mol %, fromabout 70 mol % to about 80 mol %, from about 75 mol % to about 90 mol %,from about 75 mol % to about 85 mol %, or from about 80 mol % to about90 mol % of the total lipid present in the particle.

In additional embodiments, the cationic lipid may comprise (at least)about 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,84, 85, 86, 87, 88, 89, or 90 mol % (or any fraction thereof or rangetherein) of the total lipid present in the particle.

In the lipid particles of the invention (e.g., SNALP comprising aninterfering RNA such as siRNA), the non-cationic lipid may comprise,e.g., one or more anionic lipids and/or neutral lipids. In preferredembodiments, the non-cationic lipid comprises one of the followingneutral lipid components: (1) cholesterol or a derivative thereof (2) aphospholipid; or (3) a mixture of a phospholipid and cholesterol or aderivative thereof.

Examples of cholesterol derivatives include, but are not limited to,cholestanol, cholestanone, cholestenone, coprostanol,cholesteryl-2′-hydroxyethyl ether, cholesteryl-4′-hydroxybutyl ether,and mixtures thereof. The synthesis of cholesteryl-2′-hydroxyethyl etheris described herein.

The phospholipid may be a neutral lipid including, but not limited to,dipalmitoylphosphatidylcholine (DPPC), distearoylphosphatidylcholine(DSPC), dioleoylphosphatidylethanolamine (DOPE),palmitoyloleoyl-phosphatidylcholine (POPC),palmitoyloleoyl-phosphatidylethanolamine (POPE),palmitoyloleyol-phosphatidylglycerol (POPG),dipalmitoyl-phosphatidylethanolamine (DPPE),dimyristoyl-phosphatidylethanolamine (DMPE),distearoyl-phosphatidylethanolamine (DSPE),monomethyl-phosphatidylethanolamine, dimethyl-phosphatidylethanolamine,dielaidoyl-phosphatidylethanolamine (DEPE),stearoyloleoyl-phosphatidylethanolamine (SOPE), egg phosphatidylcholine(EPC), and mixtures thereof. In certain preferred embodiments, thephospholipid is DPPC, DSPC, or mixtures thereof.

In some embodiments, the non-cationic lipid (e.g., one or morephospholipids and/or cholesterol) may comprise from about 10 mol % toabout 60 mol %, from about 15 mol % to about 60 mol %, from about 20 mol% to about 60 mol %, from about 25 mol % to about 60 mol %, from about30 mol % to about 60 mol %, from about 10 mol % to about 55 mol %, fromabout 15 mol % to about 55 mol %, from about 20 mol % to about 55 mol %,from about 25 mol % to about 55 mol %, from about 30 mol % to about 55mol %, from about 13 mol % to about 50 mol %, from about 15 mol % toabout 50 mol % or from about 20 mol % to about 50 mol % of the totallipid present in the particle. When the non-cationic lipid is a mixtureof a phospholipid and cholesterol or a cholesterol derivative, themixture may comprise up to about 40, 50, or 60 mol % of the total lipidpresent in the particle.

In other embodiments, the non-cationic lipid (e.g., one or morephospholipids and/or cholesterol) may comprise from about 10 mol % toabout 49.5 mol %, from about 13 mol % to about 49.5 mol %, from about 15mol % to about 49.5 mol %, from about 20 mol % to about 49.5 mol %, fromabout 25 mol % to about 49.5 mol %, from about 30 mol % to about 49.5mol %, from about 35 mol % to about 49.5 mol %, or from about 40 mol %to about 49.5 mol % of the total lipid present in the particle.

In yet other embodiments, the non-cationic lipid (e.g., one or morephospholipids and/or cholesterol) may comprise from about 10 mol % toabout 45 mol %, from about 13 mol % to about 45 mol %, from about 15 mol% to about 45 mol %, from about 20 mol % to about 45 mol %, from about25 mol % to about 45 mol %, from about 30 mol % to about 45 mol %, orfrom about 35 mol % to about 45 mol % of the total lipid present in theparticle.

In still yet other embodiments, the non-cationic lipid (e.g., one ormore phospholipids and/or cholesterol) may comprise from about 10 mol %to about 40 mol %, from about 13 mol % to about 40 mol %, from about 15mol % to about 40 mol %, from about 20 mol % to about 40 mol %, fromabout 25 mol % to about 40 mol %, or from about 30 mol % to about 40 mol% of the total lipid present in the particle.

In further embodiments, the non-cationic lipid (e.g., one or morephospholipids and/or cholesterol) may comprise from about 10 mol % toabout 35 mol %, from about 13 mol % to about 35 mol %, from about 15 mol% to about 35 mol %, from about 20 mol % to about 35 mol %, or fromabout 25 mol % to about 35 mol % of the total lipid present in theparticle.

In yet further embodiments, the non-cationic lipid (e.g., one or morephospholipids and/or cholesterol) may comprise from about 10 mol % toabout 30 mol %, from about 13 mol % to about 30 mol %, from about 15 mol% to about 30 mol %, from about 20 mol % to about 30 mol %, from about10 mol % to about 25 mol %, from about 13 mol % to about 25 mol %, orfrom about 15 mol % to about 25 mol % of the total lipid present in theparticle.

In additional embodiments, the non-cationic lipid (e.g., one or morephospholipids and/or cholesterol) may comprise (at least) about 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 mol % (or anyfraction thereof or range therein) of the total lipid present in theparticle.

In certain preferred embodiments, the non-cationic lipid comprisescholesterol or a derivative thereof of from about 31.5 mol % to about42.5 mol % of the total lipid present in the particle. As a non-limitingexample, a phospholipid-free lipid particle of the invention maycomprise cholesterol or a derivative thereof at about 37 mol % of thetotal lipid present in the particle. In other preferred embodiments, aphospholipid-free lipid particle of the invention may comprisecholesterol or a derivative thereof of from about 30 mol % to about 45mol %, from about 30 mol % to about 40 mol %, from about 30 mol % toabout 35 mol %, from about 35 mol % to about 45 mol %, from about 40 mol% to about 45 mol %, from about 32 mol % to about 45 mol %, from about32 mol % to about 42 mol %, from about 32 mol % to about 40 mol %, fromabout 34 mol % to about 45 mol %, from about 34 mol % to about 42 mol %,from about 34 mol % to about 40 mol %, or about 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, or 45 mol % (or any fraction thereofor range therein) of the total lipid present in the particle.

In certain other preferred embodiments, the non-cationic lipid comprisesa mixture of: (i) a phospholipid of from about 4 mol % to about 10 mol %of the total lipid present in the particle; and (ii) cholesterol or aderivative thereof of from about 30 mol % to about 40 mol % of the totallipid present in the particle. As a non-limiting example, a lipidparticle comprising a mixture of a phospholipid and cholesterol maycomprise DPPC at about 7 mol % and cholesterol at about 34 mol % of thetotal lipid present in the particle. In other embodiments, thenon-cationic lipid comprises a mixture of: (i) a phospholipid of fromabout 3 mol % to about 15 mol %, from about 4 mol % to about 15 mol %,from about 4 mol % to about 12 mol %, from about 4 mol % to about 10 mol%, from about 4 mol % to about 8 mol %, from about 5 mol % to about 12mol %, from about 5 mol % to about 9 mol %, from about 6 mol % to about12 mol %, from about 6 mol % to about 10 mol %, or about 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, or 15 mol % (or any fraction thereof or rangetherein) of the total lipid present in the particle; and (ii)cholesterol or a derivative thereof of from about 25 mol % to about 45mol %, from about 30 mol % to about 45 mol %, from about 25 mol % toabout 40 mol %, from about 30 mol % to about 40 mol %, from about 25 mol% to about 35 mol %, from about 30 mol % to about 35 mol %, from about35 mol % to about 45 mol %, from about 40 mol % to about 45 mol %, fromabout 28 mol % to about 40 mol %, from about 28 mol % to about 38 mol %,from about 30 mol % to about 38 mol %, from about 32 mol % to about 36mol %, or about 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,39, 40, 41, 42, 43, 44, or 45 mol % (or any fraction thereof or rangetherein) of the total lipid present in the particle.

In further preferred embodiments, the non-cationic lipid comprises amixture of: (i) a phospholipid of from about 10 mol % to about 30 mol %of the total lipid present in the particle; and (ii) cholesterol or aderivative thereof of from about 10 mol % to about 30 mol % of the totallipid present in the particle. As a non-limiting example, a lipidparticle comprising a mixture of a phospholipid and cholesterol maycomprise DPPC at about 20 mol % and cholesterol at about 20 mol % of thetotal lipid present in the particle. In other embodiments, thenon-cationic lipid comprises a mixture of: (i) a phospholipid of fromabout 10 mol % to about 30 mol %, from about 10 mol % to about 25 mol %,from about 10 mol % to about 20 mol %, from about 15 mol % to about 30mol %, from about 20 mol % to about 30 mol %, from about 15 mol % toabout 25 mol %, from about 12 mol % to about 28 mol %, from about 14 mol% to about 26 mol %, or about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 mol % (or any fractionthereof or range therein) of the total lipid present in the particle;and (ii) cholesterol or a derivative thereof of from about 10 mol % toabout 30 mol %, from about 10 mol % to about 25 mol %, from about 10 mol% to about 20 mol %, from about 15 mol % to about 30 mol %, from about20 mol % to about 30 mol %, from about 15 mol % to about 25 mol %, fromabout 12 mol % to about 28 mol %, from about 14 mol % to about 26 mol %,or about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, or 30 mol % (or any fraction thereof or range therein)of the total lipid present in the particle.

In the lipid particles of the invention (e.g., SNALP comprising aninterfering RNA such as siRNA), the conjugated lipid that inhibitsaggregation of particles may comprise, e.g., one or more of thefollowing: a polyethyleneglycol (PEG)-lipid conjugate, a polyamide(ATTA)-lipid conjugate, a cationic-polymer-lipid conjugates (CPLs), ormixtures thereof. In one preferred embodiment, the nucleic acid-lipidparticles comprise either a PEG-lipid conjugate or an ATTA-lipidconjugate. In certain embodiments, the PEG-lipid conjugate or ATTA-lipidconjugate is used together with a CPL. The conjugated lipid thatinhibits aggregation of particles may comprise a PEG-lipid including,e.g., a PEG-diacylglycerol (DAG), a PEG dialkyloxypropyl (DAA), aPEG-phospholipid, a PEG-ceramide (Cer), or mixtures thereof. The PEG-DAAconjugate may be PEG-dilauryloxypropyl (C12), a PEG-dimyristyloxypropyl(C14), a PEG-dipalmityloxypropyl (C16), a PEG-distearyloxypropyl (C18),or mixtures thereof.

Additional PEG-lipid conjugates suitable for use in the inventioninclude, but are not limited to,mPEG2000-1,2-di-O-alkyl-sn3-carbomoylglyceride (PEG-C-DOMG). Thesynthesis of PEG-C-DOMG is described in PCT Application No.PCT/US08/88676, filed Dec. 31, 2008, the disclosure of which is hereinincorporated by reference in its entirety for all purposes. Yetadditional PEG-lipid conjugates suitable for use in the inventioninclude, without limitation,1-[8′-(1,2-dimyristoyl-3-propanoxy)-carboxamido-3′,6′-dioxaoctanyl]carbamoyl-w-methyl-poly(ethyleneglycol) (2 KPEG-DMG). The synthesis of 2 KPEG-DMG is described in U.S.Pat. No. 7,404,969, the disclosure of which is herein incorporated byreference in its entirety for all purposes.

The PEG moiety of the PEG-lipid conjugates described herein may comprisean average molecular weight ranging from about 550 daltons to about10,000 daltons. In certain instances, the PEG moiety has an averagemolecular weight of from about 750 daltons to about 5,000 daltons (e.g.,from about 1,000 daltons to about 5,000 daltons, from about 1,500daltons to about 3,000 daltons, from about 750 daltons to about 3,000daltons, from about 750 daltons to about 2,000 daltons, etc.). Inpreferred embodiments, the PEG moiety has an average molecular weight ofabout 2,000 daltons or about 750 daltons.

In some embodiments, the conjugated lipid that inhibits aggregation ofparticles is a CPL that has the formula: A-W—Y, wherein A is a lipidmoiety, W is a hydrophilic polymer, and Y is a polycationic moiety. Wmay be a polymer selected from the group consisting ofpolyethyleneglycol (PEG), polyamide, polylactic acid, polyglycolic acid,polylactic acid/polyglycolic acid copolymers, or combinations thereof,the polymer having a molecular weight of from about 250 to about 7000daltons. In some embodiments, Y has at least 4 positive charges at aselected pH. In some embodiments, Y may be lysine, arginine, asparagine,glutamine, derivatives thereof, or combinations thereof.

In certain instances, the conjugated lipid that inhibits aggregation ofparticles (e.g., PEG-lipid conjugate) may comprise from about 0.1 mol %to about 2 mol %, from about 0.5 mol % to about 2 mol %, from about 1mol % to about 2 mol %, from about 0.6 mol % to about 1.9 mol %, fromabout 0.7 mol % to about 1.8 mol %, from about 0.8 mol % to about 1.7mol %, from about 1 mol % to about 1.8 mol %, from about 1.2 mol % toabout 1.8 mol %, from about 1.2 mol % to about 1.7 mol %, from about 1.3mol % to about 1.6 mol %, from about 1.4 mol % to about 1.5 mol %, orabout 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, or 2 mol % (or anyfraction thereof or range therein) of the total lipid present in theparticle.

In the lipid particles of the invention, the active agent or therapeuticagent may be fully encapsulated within the lipid portion of theparticle, thereby protecting the active agent or therapeutic agent fromenzymatic degradation. In preferred embodiments, a SNALP comprising anucleic acid such as an interfering RNA (e.g., siRNA) is fullyencapsulated within the lipid portion of the particle, therebyprotecting the nucleic acid from nuclease degradation. In certaininstances, the nucleic acid in the SNALP is not substantially degradedafter exposure of the particle to a nuclease at 37° C. for at leastabout 20, 30, 45, or 60 minutes. In certain other instances, the nucleicacid in the SNALP is not substantially degraded after incubation of theparticle in serum at 37° C. for at least about 30, 45, or 60 minutes orat least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24,26, 28, 30, 32, 34, or 36 hours. In other embodiments, the active agentor therapeutic agent (e.g., nucleic acid such as siRNA) is complexedwith the lipid portion of the particle. One of the benefits of theformulations of the present invention is that the lipid particlecompositions are substantially non-toxic to mammals such as humans.

The term “fully encapsulated” indicates that the active agent ortherapeutic agent in the lipid particle is not significantly degradedafter exposure to serum or a nuclease or protease assay that wouldsignificantly degrade free DNA, RNA, or protein. In a fully encapsulatedsystem, preferably less than about 25% of the active agent ortherapeutic agent in the particle is degraded in a treatment that wouldnormally degrade 100% of free active agent or therapeutic agent, morepreferably less than about 10%, and most preferably less than about 5%of the active agent or therapeutic agent in the particle is degraded. Inthe context of nucleic acid therapeutic agents, full encapsulation maybe determined by an Oligreen® assay. Oligreen® is an ultra-sensitivefluorescent nucleic acid stain for quantitating oligonucleotides andsingle-stranded DNA or RNA in solution (available from InvitrogenCorporation; Carlsbad, Calif.). “Fully encapsulated” also indicates thatthe lipid particles are serum-stable, that is, that they do not rapidlydecompose into their component parts upon in vivo administration.

In another aspect, the present invention provides a lipid particle(e.g., SNALP) composition comprising a plurality of lipid particles. Inpreferred embodiments, the active agent or therapeutic agent (e.g.,nucleic acid) is fully encapsulated within the lipid portion of thelipid particles (e.g., SNALP), such that from about 30% to about 100%,from about 40% to about 100%, from about 50% to about 100%, from about60% to about 100%, from about 70% to about 100%, from about 80% to about100%, from about 90% to about 100%, from about 30% to about 95%, fromabout 40% to about 95%, from about 50% to about 95%, from about 60% toabout 95%, %, from about 70% to about 95%, from about 80% to about 95%,from about 85% to about 95%, from about 90% to about 95%, from about 30%to about 90%, from about 40% to about 90%, from about 50% to about 90%,from about 60% to about 90%, from about 70% to about 90%, from about 80%to about 90%, or at least about 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%(or any fraction thereof or range therein) of the lipid particles (e.g.,SNALP) have the active agent or therapeutic agent encapsulated therein.

Typically, the lipid particles (e.g., SNALP) of the invention have alipid:active agent (e.g., lipid:nucleic acid) ratio (mass/mass ratio) offrom about 1 to about 100. In some instances, the lipid:active agent(e.g., lipid:nucleic acid) ratio (mass/mass ratio) ranges from about 1to about 50, from about 2 to about 25, from about 3 to about 20, fromabout 4 to about 15, or from about 5 to about 10. In preferredembodiments, the lipid particles of the invention have a lipid:activeagent (e.g., lipid:nucleic acid) ratio (mass/mass ratio) of from about 5to about 15, e.g., about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 (orany fraction thereof or range therein).

Typically, the lipid particles (e.g., SNALP) of the invention have amean diameter of from about 40 nm to about 150 nm. In preferredembodiments, the lipid particles (e.g., SNALP) of the invention have amean diameter of from about 40 nm to about 130 nm, from about 40 nm toabout 120 nm, from about 40 nm to about 100 nm, from about 50 nm toabout 120 nm, from about 50 nm to about 100 nm, from about 60 nm toabout 120 nm, from about 60 nm to about 110 nm, from about 60 nm toabout 100 nm, from about 60 nm to about 90 nm, from about 60 nm to about80 nm, from about 70 nm to about 120 nm, from about 70 nm to about 110nm, from about 70 nm to about 100 nm, from about 70 nm to about 90 nm,from about 70 nm to about 80 nm, or less than about 120 nm, 110 nm, 100nm, 90 nm, or 80 nm (or any fraction thereof or range therein).

In one specific embodiment of the invention, the SNALP comprises: (a)one or more unmodified and/or modified interfering RNA (e.g., siRNA,aiRNA, miRNA) that silence target gene expression; (b) a cationic lipidcomprising from about 56.5 mol % to about 66.5 mol % of the total lipidpresent in the particle; (c) a non-cationic lipid comprising from about31.5 mol % to about 42.5 mol % of the total lipid present in theparticle; and (d) a conjugated lipid that inhibits aggregation ofparticles comprising from about 1 mol % to about 2 mol % of the totallipid present in the particle. This specific embodiment of SNALP isgenerally referred to herein as the “1:62” formulation. In a preferredembodiment, the cationic lipid is DLinDMA or DLin-K-C2-DMA (“XTC2”), thenon-cationic lipid is cholesterol, and the conjugated lipid is a PEG-DAAconjugate. Although these are preferred embodiments of the 1:62formulation, those of skill in the art will appreciate that othercationic lipids, non-cationic lipids (including other cholesterolderivatives), and conjugated lipids can be used in the 1:62 formulationas described herein.

In another specific embodiment of the invention, the SNALP comprises:(a) one or more unmodified and/or modified interfering RNA (e.g., siRNA,aiRNA, miRNA) that silence target gene expression; (b) a cationic lipidcomprising from about 52 mol % to about 62 mol % of the total lipidpresent in the particle; (c) a non-cationic lipid comprising from about36 mol % to about 47 mol % of the total lipid present in the particle;and (d) a conjugated lipid that inhibits aggregation of particlescomprising from about 1 mol % to about 2 mol % of the total lipidpresent in the particle. This specific embodiment of SNALP is generallyreferred to herein as the “1:57” formulation. In one preferredembodiment, the cationic lipid is DLinDMA or DLin-K-C2-DMA (“XTC2”), thenon-cationic lipid is a mixture of a phospholipid (such as DPPC) andcholesterol, wherein the phospholipid comprises from about 5 mol % toabout 9 mol % of the total lipid present in the particle (e.g., about7.1 mol %) and the cholesterol (or cholesterol derivative) comprisesfrom about 32 mol % to about 37 mol % of the total lipid present in theparticle (e.g., about 34.3 mol %), and the PEG-lipid is a PEG-DAA (e.g.,PEG-cDMA). In another preferred embodiment, the cationic lipid isDLinDMA or DLin-K-C2-DMA (“XTC2”), the non-cationic lipid is a mixtureof a phospholipid (such as DPPC) and cholesterol, wherein thephospholipid comprises from about 15 mol % to about 25 mol % of thetotal lipid present in the particle (e.g., about 20 mol %) and thecholesterol (or cholesterol derivative) comprises from about 15 mol % toabout 25 mol % of the total lipid present in the particle (e.g., about20 mol %), and the PEG-lipid is a PEG-DAA (e.g., PEG-cDMA). Althoughthese are preferred embodiments of the 1:57 formulation, those of skillin the art will appreciate that other cationic lipids, non-cationiclipids (including other phospholipids and other cholesterolderivatives), and conjugated lipids can be used in the 1:57 formulationas described herein.

In preferred embodiments, the 1:62 SNALP formulation is athree-component system which is phospholipid-free and comprises about1.5 mol % PEG-cDMA (or PEG-IDSA), about 61.5 mol % DLinDMA (or XTC2),and about 36.9 mol % cholesterol (or derivative thereof). In otherpreferred embodiments, the 1:57 SNALP formulation is a four-componentsystem which comprises about 1.4 mol % PEG-cDMA (or PEG-cDSA), about57.1 mol % DLinDMA (or XTC2), about 7.1 mol % DPPC, and about 34.3 mol %cholesterol (or derivative thereof). In yet other preferred embodiments,the 1:57 SNALP formulation is a four-component system which comprisesabout 1.4 mol % PEG-cDMA (or PEG-cDSA), about 57.1 mol % DLinDMA (orXTC2), about 20 mol % DPPC, and about 20 mol % cholesterol (orderivative thereof). It should be understood that these SNALPformulations are target formulations, and that the amount of lipid (bothcationic and non-cationic) present and the amount of lipid conjugatepresent in the SNALP formulations may vary.

The present invention also provides a pharmaceutical compositioncomprising a lipid particle (e.g., SNALP) described herein and apharmaceutically acceptable carrier.

In a further aspect, the present invention provides a method forintroducing one or more active agents or therapeutic agents (e.g.,nucleic acid) into a cell, comprising contacting the cell with a lipidparticle (e.g., SNALP) described herein. In one embodiment, the cell isin a mammal and the mammal is a human. In another embodiment, thepresent invention provides a method for the in vivo delivery of one ormore active agents or therapeutic agents (e.g., nucleic acid),comprising administering to a mammalian subject a lipid particle (e.g.,SNALP) described herein. In a preferred embodiment, the mode ofadministration includes, but is not limited to, oral, intranasal,intravenous, intraperitoneal, intramuscular, intra-articular,intralesional, intratracheal, subcutaneous, and intradermal. Preferably,the mammalian subject is a human.

In one embodiment, at least about 5%, 10%, 15%, 20%, or 25% of the totalinjected dose of the lipid particles (e.g., SNALP) is present in plasmaabout 8, 12, 24, 36, or 48 hours after injection. In other embodiments,more than about 20%, 30%, 40% and as much as about 60%, 70% or 80% ofthe total injected dose of the lipid particles (e.g., SNALP) is presentin plasma about 8, 12, 24, 36, or 48 hours after injection. In certaininstances, more than about 10% of a plurality of the particles ispresent in the plasma of a mammal about 1 hour after administration. Incertain other instances, the presence of the lipid particles (e.g.,SNALP) is detectable at least about 1 hour after administration of theparticle. In certain embodiments, the presence of an active agent ortherapeutic agent such as an interfering RNA (e.g., siRNA) is detectablein cells of the lung, liver, tumor, or at a site of inflammation atabout 8, 12, 24, 36, 48, 60, 72 or 96 hours after administration. Inother embodiments, downregulation of expression of a target sequence byan active agent or therapeutic agent such as an interfering RNA (e.g.,siRNA) is detectable at about 8, 12, 24, 36, 48, 60, 72 or 96 hoursafter administration. In yet other embodiments, downregulation ofexpression of a target sequence by an active agent or therapeutic agentsuch as an interfering RNA (e.g., siRNA) occurs preferentially in tumorcells or in cells at a site of inflammation. In further embodiments, thepresence or effect of an active agent or therapeutic agent such as aninterfering RNA (e.g., siRNA) in cells at a site proximal or distal tothe site of administration or in cells of the lung, liver, or a tumor isdetectable at about 12, 24, 48, 72, or 96 hours, or at about 6, 8, 10,12, 14, 16, 18, 19, 20, 22, 24, 26, or 28 days after administration. Inadditional embodiments, the lipid particles (e.g., SNALP) of theinvention are administered parenterally or intraperitoneally.

In some embodiments, the lipid particles (e.g., SNALP) of the inventionare particularly useful in methods for the therapeutic delivery of oneor more nucleic acids comprising an interfering RNA sequence (e.g.,siRNA). In particular, it is an object of this invention to provide invitro and in vivo methods for treatment of a disease or disorder in amammal (e.g., a rodent such as a mouse or a primate such as a human,chimpanzee, or monkey) by downregulating or silencing the transcriptionand/or translation of one or more target nucleic acid sequences or genesof interest. As a non-limiting example, the methods of the invention areuseful for in vivo delivery of interfering RNA (e.g., siRNA) to theliver and/or tumor of a mammalian subject. In certain embodiments, thedisease or disorder is associated with expression and/or overexpressionof a gene and expression or overexpression of the gene is reduced by theinterfering RNA (e.g., siRNA). In certain other embodiments, atherapeutically effective amount of the lipid particle (e.g., SNALP) maybe administered to the mammal. In some instances, an interfering RNA(e.g., siRNA) is formulated into a SNALP, and the particles areadministered to patients requiring such treatment. In other instances,cells are removed from a patient, the interfering RNA (e.g., siRNA) isdelivered in vitro (e.g., using a SNALP described herein), and the cellsare reinjected into the patient.

In an additional aspect, the present invention provides lipid particles(e.g., SNALP) comprising asymmetrical interfering RNA (aiRNA) moleculesthat silence the expression of a target gene and methods of using suchparticles to silence target gene expression.

In one embodiment, the aiRNA molecule comprises a double-stranded(duplex) region of about 10 to about 25 (base paired) nucleotides inlength, wherein the aiRNA molecule comprises an antisense strandcomprising 5′ and 3′ overhangs, and wherein the aiRNA molecule iscapable of silencing target gene expression.

In certain instances, the aiRNA molecule comprises a double-stranded(duplex) region of about 12-20, 12-19, 12-18, 13-17, or 14-17 (basepaired) nucleotides in length, more typically 12, 13, 14, 15, 16, 17,18, 19, or 20 (base paired) nucleotides in length. In certain otherinstances, the 5′ and 3′ overhangs on the antisense strand comprisesequences that are complementary to the target RNA sequence, and mayoptionally further comprise nontargeting sequences. In some embodiments,each of the 5′ and 3′ overhangs on the antisense strand comprises orconsists of one, two, three, four, five, six, seven, or morenucleotides.

In other embodiments, the aiRNA molecule comprises modified nucleotidesselected from the group consisting of 2′OMe nucleotides, 2′Fnucleotides, 2′-deoxy nucleotides, 2′-O-MOE nucleotides, LNAnucleotides, and mixtures thereof. In a preferred embodiment, the aiRNAmolecule comprises 2′OMe nucleotides. As a non-limiting example, the2′OMe nucleotides may be selected from the group consisting of2′OMe-guanosine nucleotides, 2′OMe-uridine nucleotides, and mixturesthereof.

In a related aspect, the present invention provides lipid particles(e.g., SNALP) comprising microRNA (miRNA) molecules that silence theexpression of a target gene and methods of using such compositions tosilence target gene expression.

In one embodiment, the miRNA molecule comprises about 15 to about 60nucleotides in length, wherein the miRNA molecule is capable ofsilencing target gene expression.

In certain instances, the miRNA molecule comprises about 15-50, 15-40,or 15-30 nucleotides in length, more typically about 15-25 or 19-25nucleotides in length, and are preferably about 20-24, 21-22, or 21-23nucleotides in length. In a preferred embodiment, the miRNA molecule isa mature miRNA molecule targeting an RNA sequence of interest.

In some embodiments, the miRNA molecule comprises modified nucleotidesselected from the group consisting of 2′OMe nucleotides, 2′Fnucleotides, 2′-deoxy nucleotides, 2′-O-MOE nucleotides, LNAnucleotides, and mixtures thereof. In a preferred embodiment, the miRNAmolecule comprises 2′OMe nucleotides. As a non-limiting example, the2′OMe nucleotides may be selected from the group consisting of2′OMe-guanosine nucleotides, 2′OMe-uridine nucleotides, and mixturesthereof.

As such, the lipid particles of the invention (e.g., SNALP) areadvantageous and suitable for use in the administration of active agentsor therapeutic agents such as nucleic acid (e.g., interfering RNA suchas siRNA, aiRNA, and/or miRNA) to a subject (e.g., a mammal such as ahuman) because they are stable in circulation, of a size required forpharmacodynamic behavior resulting in access to extravascular sites, andare capable of reaching target cell populations.

IV. Active Agents

Active agents (e.g., therapeutic agents) include any molecule orcompound capable of exerting a desired effect on a cell, tissue, organ,or subject. Such effects may be, e.g., biological, physiological, and/orcosmetic. Active agents may be any type of molecule or compoundincluding, but not limited to, nucleic acids, peptides, polypeptides,small molecules, and mixtures thereof. Non-limiting examples of nucleicacids include interfering RNA molecules (e.g., siRNA, aiRNA, miRNA),antisense oligonucleotides, plasmids, ribozymes, immunostimulatoryoligonucleotides, and mixtures thereof. Examples of peptides orpolypeptides include, without limitation, antibodies (e.g., polyclonalantibodies, monoclonal antibodies, antibody fragments; humanizedantibodies, recombinant antibodies, recombinant human antibodies,Primatized™ antibodies), cytokines, growth factors, apoptotic factors,differentiation-inducing factors, cell-surface receptors and theirligands, hormones, and mixtures thereof. Examples of small moleculesinclude, but are not limited to, small organic molecules or compoundssuch as any conventional agent or drug known to those of skill in theart.

In some embodiments, the active agent is a therapeutic agent, or a saltor derivative thereof. Therapeutic agent derivatives may betherapeutically active themselves or they may be prodrugs, which becomeactive upon further modification. Thus, in one embodiment, a therapeuticagent derivative retains some or all of the therapeutic activity ascompared to the unmodified agent, while in another embodiment, atherapeutic agent derivative is a prodrug that lacks therapeuticactivity, but becomes active upon further modification.

A. Nucleic Acids

In certain embodiments, lipid particles of the present invention areassociated with a nucleic acid, resulting in a nucleic acid-lipidparticle (e.g., SNALP). In some embodiments, the nucleic acid is fullyencapsulated in the lipid particle. As used herein, the term “nucleicacid” includes any oligonucleotide or polynucleotide, with fragmentscontaining up to 60 nucleotides generally termed oligonucleotides, andlonger fragments termed polynucleotides. In particular embodiments,oligonucletoides of the invention are from about 15 to about 60nucleotides in length. Nucleic acid may be administered alone in thelipid particles of the invention, or in combination (e.g.,co-administered) with lipid particles of the invention comprisingpeptides, polypeptides, or small molecules such as conventional drugs.

In the context of this invention, the terms “polynucleotide” and“oligonucleotide” refer to a polymer or oligomer of nucleotide ornucleoside monomers consisting of naturally-occurring bases, sugars andintersugar (backbone) linkages. The terms “polynucleotide” and“oligonucleotide” also include polymers or oligomers comprisingnon-naturally occurring monomers, or portions thereof, which functionsimilarly. Such modified or substituted oligonucleotides are oftenpreferred over native forms because of properties such as, for example,enhanced cellular uptake, reduced immunogenicity, and increasedstability in the presence of nucleases.

Oligonucleotides are generally classified as deoxyribooligonucleotidesor ribooligonucleotides. A deoxyribooligonucleotide consists of a5-carbon sugar called deoxyribose joined covalently to phosphate at the5′ and 3′ carbons of this sugar to form an alternating, unbranchedpolymer. A ribooligonucleotide consists of a similar repeating structurewhere the 5-carbon sugar is ribose.

The nucleic acid that is present in a lipid-nucleic acid particleaccording to this invention includes any form of nucleic acid that isknown. The nucleic acids used herein can be single-stranded DNA or RNA,or double-stranded DNA or RNA, or DNA-RNA hybrids. Examples ofdouble-stranded DNA are described herein and include, e.g., structuralgenes, genes including control and termination regions, andself-replicating systems such as viral or plasmid DNA. Examples ofdouble-stranded RNA are described herein and include, e.g., siRNA andother RNAi agents such as aiRNA and pre-miRNA. Single-stranded nucleicacids include, e.g., antisense oligonucleotides, ribozymes, maturemiRNA, and triplex-forming oligonucleotides.

Nucleic acids of the invention may be of various lengths, generallydependent upon the particular form of nucleic acid. For example, inparticular embodiments, plasmids or genes may be from about 1,000 toabout 100,000 nucleotide residues in length. In particular embodiments,oligonucleotides may range from about 10 to about 100 nucleotides inlength. In various related embodiments, oligonucleotides, bothsingle-stranded, double-stranded, and triple-stranded, may range inlength from about 10 to about 60 nucleotides, from about 15 to about 60nucleotides, from about 20 to about 50 nucleotides, from about 15 toabout 30 nucleotides, or from about 20 to about 30 nucleotides inlength.

In particular embodiments, an oligonucleotide (or a strand thereof) ofthe invention specifically hybridizes to or is complementary to a targetpolynucleotide sequence. The terms “specifically hybridizable” and“complementary” as used herein indicate a sufficient degree ofcomplementarity such that stable and specific binding occurs between theDNA or RNA target and the oligonucleotide. It is understood that anoligonucleotide need not be 100% complementary to its target nucleicacid sequence to be specifically hybridizable. In preferred embodiments,an oligonucleotide is specifically hybridizable when binding of theoligonucleotide to the target sequence interferes with the normalfunction of the target sequence to cause a loss of utility or expressiontherefrom, and there is a sufficient degree of complementarity to avoidnon-specific binding of the oligonucleotide to non-target sequencesunder conditions in which specific binding is desired, i.e., underphysiological conditions in the case of in vivo assays or therapeutictreatment, or, in the case of in vitro assays, under conditions in whichthe assays are conducted. Thus, the oligonucleotide may include 1, 2, 3,or more base substitutions as compared to the region of a gene or mRNAsequence that it is targeting or to which it specifically hybridizes.

1. siRNA

The siRNA component of the nucleic acid-lipid particles of the presentinvention is capable of silencing the expression of a target gene ofinterest. Each strand of the siRNA duplex is typically about 15 to about60 nucleotides in length, preferably about 15 to about 30 nucleotides inlength. In certain embodiments, the siRNA comprises at least onemodified nucleotide. The modified siRNA is generally lessimmunostimulatory than a corresponding unmodified siRNA sequence andretains RNAi activity against the target gene of interest. In someembodiments, the modified siRNA contains at least one 2′OMe purine orpyrimidine nucleotide such as a 2′OMe-guanosine, 2′OMe-uridine,2′OMe-adenosine, and/or 2′OMe-cytosine nucleotide. In preferredembodiments, one or more of the uridine and/or guanosine nucleotides aremodified. The modified nucleotides can be present in one strand (i.e.,sense or antisense) or both strands of the siRNA. The siRNA sequencesmay have overhangs (e.g., 3′ or 5′ overhangs as described in Elbashir etal., Genes Dev., 15:188 (2001) or Nykänen et al., Cell, 107:309 (2001)),or may lack overhangs (i.e., have blunt ends).

The modified siRNA generally comprises from about 1% to about 100%(e.g., about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%,14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%,28%, 29%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95%, or 100%) modified nucleotides in the double-stranded region ofthe siRNA duplex. In certain embodiments, one, two, three, four, five,six, seven, eight, nine, ten, or more of the nucleotides in thedouble-stranded region of the siRNA comprise modified nucleotides.

In some embodiments, less than about 25% (e.g., less than about 25%,24%, 23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%,10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1%) of the nucleotides in thedouble-stranded region of the siRNA comprise modified nucleotides.

In other embodiments, from about 1% to about 25% (e.g., from about1%-25%, 2%-25%, 3%-25%, 4%-25%, 5%-25%, 6%-25%, 7%-25%, 8%-25%, 9%-25%,10%-25%, 11%-25%, 12%-25%, 13%-25%, 14%-25%, 15%-25%, 16%-25%, 17%-25%,18%-25%, 19%-25%, 20%-25%, 21%-25%, 22%-25%, 23%-25%, 24%-25%, etc.) orfrom about 1% to about 20% (e.g., from about 1%-20%, 2%-20%, 3%-20%,4%-20%, 5%-20%, 6%-20%, 7%-20%, 8%-20%, 9%-20%, 10%-20%, 11%-20%,12%-20%, 13%-20%, 14%-20%, 15%-20%, 16%-20%, 17%-20%, 18%-20%, 19%-20%,1%-19%, 2%-19%, 3%-19%, 4%-19%, 5%-19%, 6%-19%, 7%-19%, 8%-19%, 9%-19%,10%-19%, 11%-19%, 12%-19%, 13%-19%, 14%-19%, 15%-19%, 16%-19%, 17%-19%,18%-19%, 1%-18%, 2%-18%, 3%-18%, 4%-18%, 5%-18%, 6%-18%, 7%-18%, 8%-18%,9%-18%, 10%-18%, 11%-18%, 12%-18%, 13%-18%, 14%-18%, 15%-18%, 16%-18%,17%-18%, 1%-17%, 2%-17%, 3%-17%, 4%-17%, 5%-17%, 6%-17%, 7%-17%, 8%-17%,9%-17%, 10%-17%, 11%-17%, 12%-17%, 13%-17%, 14%-17%, 15%-17%, 16%-17%,1%-16%, 2%-16%, 3%-16%, 4%-16%, 5%-16%, 6%-16%, 7%-16%, 8%-16%, 9%-16%,10%-16%, 11%-16%, 12%-16%, 13%-16%, 14%-16%, 15%-16%, 1%-15%, 2%-15%,3%-15%, 4%-15%, 5%-15%, 6%-15%, 7%-15%, 8%-15%, 9%-15%, 10%-15%,11%-15%, 12%-15%, 13%-15%, 14%-15%, etc.) of the nucleotides in thedouble-stranded region of the siRNA comprise modified nucleotides.

In further embodiments, e.g., when one or both strands of the siRNA areselectively modified at uridine and/or guanosine nucleotides, theresulting modified siRNA can comprise less than about 30% modifiednucleotides (e.g., less than about 30%, 29%, 28%, 27%, 26%, 25%, 24%,23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%,9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% modified nucleotides) or fromabout 1% to about 30% modified nucleotides (e.g., from about 1%-30%,2%-30%, 3%-30%, 4%-30%, 5%-30%, 6%-30%, 7%-30%, 8%-30%, 9%-30%, 10%-30%,11%-30%, 12%-30%, 13%-30%, 14%-30%, 15%-30%, 16%-30%, 17%-30%, 18%-30%,19%-30%, 20%-30%, 21%-30%, 22%-30%, 23%-30%, 24%-30%, 25%-30%, 26%-30%,27%-30%, 28%-30%, or 29%-30% modified nucleotides).

a. Selection of siRNA Sequences

Suitable siRNA sequences can be identified using any means known in theart. Typically, the methods described in Elbashir et al., Nature,411:494-498 (2001) and Elbashir et al., EMBO J., 20:6877-6888 (2001) arecombined with rational design rules set forth in Reynolds et al., NatureBiotech., 22(3):326-330 (2004).

Generally, the nucleotide sequence 3′ of the AUG start codon of atranscript from the target gene of interest is scanned for dinucleotidesequences (e.g., AA, NA, CC, GG, or UU, wherein N═C, G, or U) (see,e.g., Elbashir et al., EMBO J., 20:6877-6888 (2001)). The nucleotidesimmediately 3′ to the dinucleotide sequences are identified as potentialsiRNA sequences (i.e., a target sequence or a sense strand sequence).Typically, the 19, 21, 23, 25, 27, 29, 31, 33, 35, or more nucleotidesimmediately 3′ to the dinucleotide sequences are identified as potentialsiRNA sequences. In some embodiments, the dinucleotide sequence is an AAor NA sequence and the 19 nucleotides immediately 3′ to the AA or NAdinucleotide are identified as potential siRNA sequences. siRNAsequences are usually spaced at different positions along the length ofthe target gene. To further enhance silencing efficiency of the siRNAsequences, potential siRNA sequences may be analyzed to identify sitesthat do not contain regions of homology to other coding sequences, e.g.,in the target cell or organism. For example, a suitable siRNA sequenceof about 21 base pairs typically will not have more than 16-17contiguous base pairs of homology to coding sequences in the target cellor organism. If the siRNA sequences are to be expressed from an RNA PolIII promoter, siRNA sequences lacking more than 4 contiguous A's or T'sare selected.

Once a potential siRNA sequence has been identified, a complementarysequence (i.e., an antisense strand sequence) can be designed. Apotential siRNA sequence can also be analyzed using a variety ofcriteria known in the art. For example, to enhance their silencingefficiency, the siRNA sequences may be analyzed by a rational designalgorithm to identify sequences that have one or more of the followingfeatures: (1) G/C content of about 25% to about 60% G/C; (2) at least 3A/Us at positions 15-19 of the sense strand; (3) no internal repeats;(4) an A at position 19 of the sense strand; (5) an A at position 3 ofthe sense strand; (6) a U at position 10 of the sense strand; (7) no G/Cat position 19 of the sense strand; and (8) no G at position 13 of thesense strand. siRNA design tools that incorporate algorithms that assignsuitable values of each of these features and are useful for selectionof siRNA can be found at, e.g., http://boz094.ust.hk/RNAi/siRNA. One ofskill in the art will appreciate that sequences with one or more of theforegoing characteristics may be selected for further analysis andtesting as potential siRNA sequences.

Additionally, potential siRNA sequences with one or more of thefollowing criteria can often be eliminated as siRNA: (1) sequencescomprising a stretch of 4 or more of the same base in a row; (2)sequences comprising homopolymers of Gs (i.e., to reduce possiblenon-specific effects due to structural characteristics of thesepolymers; (3) sequences comprising triple base motifs (e.g., GGG, CCC,AAA, or TTT); (4) sequences comprising stretches of 7 or more G/Cs in arow; and (5) sequences comprising direct repeats of 4 or more baseswithin the candidates resulting in internal fold-back structures.However, one of skill in the art will appreciate that sequences with oneor more of the foregoing characteristics may still be selected forfurther analysis and testing as potential siRNA sequences.

In some embodiments, potential siRNA sequences may be further analyzedbased on siRNA duplex asymmetry as described in, e.g., Khvorova et al.,Cell, 115:209-216 (2003); and Schwarz et al., Cell, 115:199-208 (2003).In other embodiments, potential siRNA sequences may be further analyzedbased on secondary structure at the target site as described in, e.g.,Luo et al., Biophys. Res. Commun., 318:303-310 (2004). For example,secondary structure at the target site can be modeled using the Mfoldalgorithm (available athttp://www.bioinfo.rpi.edu/applications/mfold/rna/form1.cgi) to selectsiRNA sequences which favor accessibility at the target site where lesssecondary structure in the form of base-pairing and stem-loops ispresent.

Once a potential siRNA sequence has been identified, the sequence can beanalyzed for the presence of any immunostimulatory properties, e.g.,using an in vitro cytokine assay or an in vivo animal model. Motifs inthe sense and/or antisense strand of the siRNA sequence such as GU-richmotifs (e.g., 5′-GU-3′,5′-UGU-3′,5′-GUGU-3′,5′-UGUGU-3′, etc.) can alsoprovide an indication of whether the sequence may be immunostimulatory.Once an siRNA molecule is found to be immunostimulatory, it can then bemodified to decrease its immunostimulatory properties as describedherein. As a non-limiting example, an siRNA sequence can be contactedwith a mammalian responder cell under conditions such that the cellproduces a detectable immune response to determine whether the siRNA isan immunostimulatory or a non-immunostimulatory siRNA. The mammalianresponder cell may be from a naïve mammal (i.e., a mammal that has notpreviously been in contact with the gene product of the siRNA sequence).The mammalian responder cell may be, e.g., a peripheral bloodmononuclear cell (PBMC), a macrophage, and the like. The detectableimmune response may comprise production of a cytokine or growth factorsuch as, e.g., TNF-α, IFN-α, IFN-β, IFN-γ, IL-6, IL-12, or a combinationthereof. An siRNA molecule identified as being immunostimulatory canthen be modified to decrease its immunostimulatory properties byreplacing at least one of the nucleotides on the sense and/or antisensestrand with modified nucleotides. For example, less than about 30%(e.g., less than about 30%, 25%, 20%, 15%, 10%, or 5%) of thenucleotides in the double-stranded region of the siRNA duplex can bereplaced with modified nucleotides such as 2′OMe nucleotides. Themodified siRNA can then be contacted with a mammalian responder cell asdescribed above to confirm that its immunostimulatory properties havebeen reduced or abrogated.

Suitable in vitro assays for detecting an immune response include, butare not limited to, the double monoclonal antibody sandwich immunoassaytechnique of David et al. (U.S. Pat. No. 4,376,110);monoclonal-polyclonal antibody sandwich assays (Wide et al., in Kirkhamand Hunter, eds., Radioimmunoassay Methods, E. and S. Livingstone,Edinburgh (1970)); the “Western blot” method of Gordon et al. (U.S. Pat.No. 4,452,901); immunoprecipitation of labeled ligand (Brown et al., J.Biol. Chem., 255:4980-4983 (1980)); enzyme-linked immunosorbent assays(ELISA) as described, for example, by Raines et al., J. Biol. Chem.,257:5154-5160 (1982); immunocytochemical techniques, including the useof fluorochromes (Brooks et al., Clin. Exp. Immunol., 39:477 (1980));and neutralization of activity (Bowen-Pope et al., Proc. Natl. Acad.Sci. USA, 81:2396-2400 (1984)). In addition to the immunoassaysdescribed above, a number of other immunoassays are available, includingthose described in U.S. Pat. Nos. 3,817,827; 3,850,752; 3,901,654;3,935,074; 3,984,533; 3,996,345; 4,034,074; and 4,098,876. Thedisclosures of these references are herein incorporated by reference intheir entirety for all purposes.

A non-limiting example of an in vivo model for detecting an immuneresponse includes an in vivo mouse cytokine induction assay as describedin, e.g., Judge et al., Mol. Ther., 13:494-505 (2006). In certainembodiments, the assay that can be performed as follows: (1) siRNA canbe administered by standard intravenous injection in the lateral tailvein; (2) blood can be collected by cardiac puncture about 6 hours afteradministration and processed as plasma for cytokine analysis; and (3)cytokines can be quantified using sandwich ELISA kits according to themanufacturer's instructions (e.g., mouse and human IFN-α (PBLBiomedical; Piscataway, N.J.); human IL-6 and TNF-α (eBioscience; SanDiego, Calif.); and mouse IL-6, TNF-α, and IFN-γ (BD Biosciences; SanDiego, Calif.)).

Monoclonal antibodies that specifically bind cytokines and growthfactors are commercially available from multiple sources and can begenerated using methods known in the art (see, e.g., Kohler et al.,Nature, 256: 495-497 (1975) and Harlow and Lane, ANTIBODIES, ALABORATORY MANUAL, Cold Spring Harbor Publication, New York (1999)).Generation of monoclonal antibodies has been previously described andcan be accomplished by any means known in the art (Buhring et al., inHybridoma, Vol. 10, No. 1, pp. 77-78 (1991)). In some methods, themonoclonal antibody is labeled (e.g., with any composition detectable byspectroscopic, photochemical, biochemical, electrical, optical, orchemical means) to facilitate detection.

b. Generating siRNA Molecules

siRNA can be provided in several forms including, e.g., as one or moreisolated small-interfering RNA (siRNA) duplexes, as longerdouble-stranded RNA (dsRNA), or as siRNA or dsRNA transcribed from atranscriptional cassette in a DNA plasmid. The siRNA sequences may haveoverhangs (e.g., 3′ or 5′ overhangs as described in Elbashir et al.,Genes Dev., 15:188 (2001) or Nykänen et al., Cell, 107:309 (2001), ormay lack overhangs (i.e., to have blunt ends).

An RNA population can be used to provide long precursor RNAs, or longprecursor RNAs that have substantial or complete identity to a selectedtarget sequence can be used to make the siRNA. The RNAs can be isolatedfrom cells or tissue, synthesized, and/or cloned according to methodswell known to those of skill in the art. The RNA can be a mixedpopulation (obtained from cells or tissue, transcribed from cDNA,subtracted, selected, etc.), or can represent a single target sequence.RNA can be naturally occurring (e.g., isolated from tissue or cellsamples), synthesized in vitro (e.g., using T7 or SP6 polymerase and PCRproducts or a cloned cDNA), or chemically synthesized.

To form a long dsRNA, for synthetic RNAs, the complement is alsotranscribed in vitro and hybridized to form a dsRNA. If a naturallyoccurring RNA population is used, the RNA complements are also provided(e.g., to form dsRNA for digestion by E. coli RNAse III or Dicer), e.g.,by transcribing cDNAs corresponding to the RNA population, or by usingRNA polymerases. The precursor RNAs are then hybridized to form doublestranded RNAs for digestion. The dsRNAs can be directly administered toa subject or can be digested in vitro prior to administration.

Methods for isolating RNA, synthesizing RNA, hybridizing nucleic acids,making and screening cDNA libraries, and performing PCR are well knownin the art (see, e.g., Gubler and Hoffman, Gene, 25:263-269 (1983);Sambrook et al., supra; Ausubel et al., supra), as are PCR methods (see,U.S. Pat. Nos. 4,683,195 and 4,683,202; PCR Protocols: A Guide toMethods and Applications (Innis et al., eds, 1990)). Expressionlibraries are also well known to those of skill in the art. Additionalbasic texts disclosing the general methods of use in this inventioninclude Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd ed.1989); Kriegler, Gene Transfer and Expression: A Laboratory Manual(1990); and Current Protocols in Molecular Biology (Ausubel et al.,eds., 1994). The disclosures of these references are herein incorporatedby reference in their entirety for all purposes.

Preferably, siRNA are chemically synthesized. The oligonucleotides thatcomprise the siRNA molecules of the invention can be synthesized usingany of a variety of techniques known in the art, such as those describedin Usman et al., J. Am. Chem. Soc., 109:7845 (1987); Scaringe et al.,Nucl. Acids Res., 18:5433 (1990); Wincott et al., Nucl. Acids Res.,23:2677-2684 (1995); and Wincott et al., Methods Mol. Bio., 74:59(1997). The synthesis of oligonucleotides makes use of common nucleicacid protecting and coupling groups, such as dimethoxytrityl at the5′-end and phosphoramidites at the 3′-end. As a non-limiting example,small scale syntheses can be conducted on an Applied Biosystemssynthesizer using a 0.2 μmol scale protocol. Alternatively, syntheses atthe 0.2 μmol scale can be performed on a 96-well plate synthesizer fromProtogene (Palo Alto, Calif.). However, a larger or smaller scale ofsynthesis is also within the scope of this invention. Suitable reagentsfor oligonucleotide synthesis, methods for RNA deprotection, and methodsfor RNA purification are known to those of skill in the art.

siRNA molecules can also be synthesized via a tandem synthesistechnique, wherein both strands are synthesized as a single continuousoligonucleotide fragment or strand separated by a cleavable linker thatis subsequently cleaved to provide separate fragments or strands thathybridize to form the siRNA duplex. The linker can be a polynucleotidelinker or a non-nucleotide linker. The tandem synthesis of siRNA can bereadily adapted to both multiwell/multiplate synthesis platforms as wellas large scale synthesis platforms employing batch reactors, synthesiscolumns, and the like. Alternatively, siRNA molecules can be assembledfrom two distinct oligonucleotides, wherein one oligonucleotidecomprises the sense strand and the other comprises the antisense strandof the siRNA. For example, each strand can be synthesized separately andjoined together by hybridization or ligation following synthesis and/ordeprotection. In certain other instances, siRNA molecules can besynthesized as a single continuous oligonucleotide fragment, where theself-complementary sense and antisense regions hybridize to form ansiRNA duplex having hairpin secondary structure.

c. Modifying siRNA Sequences

In certain aspects, siRNA molecules comprise a duplex having two strandsand at least one modified nucleotide in the double-stranded region,wherein each strand is about 15 to about 60 nucleotides in length.Advantageously, the modified siRNA is less immunostimulatory than acorresponding unmodified siRNA sequence, but retains the capability ofsilencing the expression of a target sequence. In preferred embodiments,the degree of chemical modifications introduced into the siRNA moleculestrikes a balance between reduction or abrogation of theimmunostimulatory properties of the siRNA and retention of RNAiactivity. As a non-limiting example, an siRNA molecule that targets agene of interest can be minimally modified (e.g., less than about 30%,25%, 20%, 15%, 10%, or 5% modified) at selective uridine and/orguanosine nucleotides within the siRNA duplex to eliminate the immuneresponse generated by the siRNA while retaining its capability tosilence target gene expression.

Examples of modified nucleotides suitable for use in the inventioninclude, but are not limited to, ribonucleotides having a 2′-O-methyl(2′OMe), 2′-deoxy-2′-fluoro (2′F), 2′-deoxy, 5-C-methyl,2′-O-(2-methoxyethyl) (MOE), 4′-thio, 2′-amino, or 2′-C-allyl group.Modified nucleotides having a Northern conformation such as thosedescribed in, e.g., Saenger, Principles of Nucleic Acid Structure,Springer-Verlag Ed. (1984), are also suitable for use in siRNAmolecules. Such modified nucleotides include, without limitation, lockednucleic acid (LNA) nucleotides (e.g., 2′-O,4′-C-methylene-(D-ribofuranosyl) nucleotides), 2′-O-(2-methoxyethyl)(MOE) nucleotides, 2′-methyl-thio-ethyl nucleotides, 2′-deoxy-2′-fluoro(2′F) nucleotides, 2′-deoxy-2′-chloro (2′Cl) nucleotides, and 2′-azidonucleotides. In certain instances, the siRNA molecules described hereininclude one or more G-clamp nucleotides. A G-clamp nucleotide refers toa modified cytosine analog wherein the modifications confer the abilityto hydrogen bond both Watson-Crick and Hoogsteen faces of acomplementary guanine nucleotide within a duplex (see, e.g., Lin et al.,J. Am. Chem. Soc., 120:8531-8532 (1998)). In addition, nucleotideshaving a nucleotide base analog such as, for example, C-phenyl,C-naphthyl, other aromatic derivatives, inosine, azole carboxamides, andnitroazole derivatives such as 3-nitropyrrole, 4-nitroindole,5-nitroindole, and 6-nitroindole (see, e.g., Loakes, Nucl. Acids Res.,29:2437-2447 (2001)) can be incorporated into siRNA molecules.

In certain embodiments, siRNA molecules may further comprise one or morechemical modifications such as terminal cap moieties, phosphate backbonemodifications, and the like. Examples of terminal cap moieties include,without limitation, inverted deoxy abasic residues, glycerylmodifications, 4′,5′-methylene nucleotides, 1-(β-D-erythrofuranosyl)nucleotides, 4′-thio nucleotides, carbocyclic nucleotides,1,5-anhydrohexitol nucleotides, L-nucleotides, α-nucleotides, modifiedbase nucleotides, threo-pentofuranosyl nucleotides, acyclic 3′,4′-seconucleotides, acyclic 3,4-dihydroxybutyl nucleotides, acyclic3,5-dihydroxypentyl nucleotides, 3′-3′-inverted nucleotide moieties,3′-3′-inverted abasic moieties, 3′-2′-inverted nucleotide moieties,3′-2′-inverted abasic moieties, 5′-5′-inverted nucleotide moieties,5′-5′-inverted abasic moieties, 3′-5′-inverted deoxy abasic moieties,5′-amino-alkyl phosphate, 1,3-diamino-2-propyl phosphate, 3-aminopropylphosphate, 6-aminohexyl phosphate, 1,2-aminododecyl phosphate,hydroxypropyl phosphate, 1,4-butanediol phosphate, 3′-phosphoramidate,5′-phosphoramidate, hexylphosphate, aminohexyl phosphate, 3′-phosphate,5′-amino, 3′-phosphorothioate, 5′-phosphorothioate, phosphorodithioate,and bridging or non-bridging methylphosphonate or 5′-mercapto moieties(see, e.g., U.S. Pat. No. 5,998,203; Beaucage et al., Tetrahedron49:1925 (1993)). Non-limiting examples of phosphate backbonemodifications (i.e., resulting in modified internucleotide linkages)include phosphorothioate, phosphorodithioate, methylphosphonate,phosphotriester, morpholino, amidate, carbamate, carboxymethyl,acetamidate, polyamide, sulfonate, sulfonamide, sulfamate, formacetal,thioformacetal, and alkylsilyl substitutions (see, e.g., Hunziker etal., Nucleic Acid Analogues: Synthesis and Properties, in ModernSynthetic Methods, VCH, 331-417 (1995); Mesmaeker et al., Novel BackboneReplacements for Oligonucleotides, in Carbohydrate Modifications inAntisense Research, ACS, 24-39 (1994)). Such chemical modifications canoccur at the 5′-end and/or 3′-end of the sense strand, antisense strand,or both strands of the siRNA. The disclosures of these references areherein incorporated by reference in their entirety for all purposes.

In some embodiments, the sense and/or antisense strand of the siRNAmolecule can further comprise a 3′-terminal overhang having about 1 toabout 4 (e.g., 1, 2, 3, or 4) 2′-deoxy ribonucleotides and/or anycombination of modified and unmodified nucleotides. Additional examplesof modified nucleotides and types of chemical modifications that can beintroduced into siRNA molecules are described, e.g., in UK Patent No. GB2,397,818 B and U.S. Patent Publication Nos. 20040192626, 20050282188,and 20070135372, the disclosures of which are herein incorporated byreference in their entirety for all purposes.

The siRNA molecules described herein can optionally comprise one or morenon-nucleotides in one or both strands of the siRNA. As used herein, theterm “non-nucleotide” refers to any group or compound that can beincorporated into a nucleic acid chain in the place of one or morenucleotide units, including sugar and/or phosphate substitutions, andallows the remaining bases to exhibit their activity. The group orcompound is abasic in that it does not contain a commonly recognizednucleotide base such as adenosine, guanine, cytosine, uracil, or thymineand therefore lacks a base at the l′-position.

In other embodiments, chemical modification of the siRNA comprisesattaching a conjugate to the siRNA molecule. The conjugate can beattached at the 5′ and/or 3′-end of the sense and/or antisense strand ofthe siRNA via a covalent attachment such as, e.g., a biodegradablelinker. The conjugate can also be attached to the siRNA, e.g., through acarbamate group or other linking group (see, e.g., U.S. PatentPublication Nos. 20050074771, 20050043219, and 20050158727). In certaininstances, the conjugate is a molecule that facilitates the delivery ofthe siRNA into a cell. Examples of conjugate molecules suitable forattachment to siRNA include, without limitation, steroids such ascholesterol, glycols such as polyethylene glycol (PEG), human serumalbumin (HSA), fatty acids, carotenoids, terpenes, bile acids, folates(e.g., folic acid, folate analogs and derivatives thereof), sugars(e.g., galactose, galactosamine, N-acetyl galactosamine, glucose,mannose, fructose, fucose, etc.), phospholipids, peptides, ligands forcellular receptors capable of mediating cellular uptake, andcombinations thereof (see, e.g., U.S. Patent Publication Nos.20030130186, 20040110296, and 20040249178; U.S. Pat. No. 6,753,423).Other examples include the lipophilic moiety, vitamin, polymer, peptide,protein, nucleic acid, small molecule, oligosaccharide, carbohydratecluster, intercalator, minor groove binder, cleaving agent, andcross-linking agent conjugate molecules described in U.S. PatentPublication Nos. 20050119470 and 20050107325. Yet other examples includethe 2′-O-alkyl amine, 2′-β-alkoxyalkyl amine, polyamine, C5-cationicmodified pyrimidine, cationic peptide, guanidinium group, amidininiumgroup, cationic amino acid conjugate molecules described in U.S. PatentPublication No. 20050153337. Additional examples include the hydrophobicgroup, membrane active compound, cell penetrating compound, celltargeting signal, interaction modifier, and steric stabilizer conjugatemolecules described in U.S. Patent Publication No. 20040167090. Furtherexamples include the conjugate molecules described in U.S. PatentPublication No. 20050239739. The type of conjugate used and the extentof conjugation to the siRNA molecule can be evaluated for improvedpharmacokinetic profiles, bioavailability, and/or stability of the siRNAwhile retaining RNAi activity. As such, one skilled in the art canscreen siRNA molecules having various conjugates attached thereto toidentify ones having improved properties and full RNAi activity usingany of a variety of well-known in vitro cell culture or in vivo animalmodels. The disclosures of the above-described patent documents areherein incorporated by reference in their entirety for all purposes.

d. Target Genes

The siRNA component of the nucleic acid-lipid particles described hereincan be used to downregulate or silence the translation (i.e.,expression) of a gene of interest. Genes of interest include, but arenot limited to, genes associated with viral infection and survival,genes associated with metabolic diseases and disorders (e.g., liverdiseases and disorders), genes associated with tumorigenesis and celltransformation (e.g., cancer), angiogenic genes, immunomodulator genessuch as those associated with inflammatory and autoimmune responses,ligand receptor genes, and genes associated with neurodegenerativedisorders.

Genes associated with viral infection and survival include thoseexpressed by a virus in order to bind, enter, and replicate in a cell.Of particular interest are viral sequences associated with chronic viraldiseases. Viral sequences of particular interest include sequences ofFiloviruses such as Ebola virus and Marburg virus (see, e.g., Geisbertet al., J. Infect. Dis., 193:1650-1657 (2006)); Arenaviruses such asLassa virus, Junin virus, Machupo virus, Guanarito virus, and Sabiavirus (Buchmeier et al., Arenaviridae: the viruses and theirreplication, In: FIELDS VIROLOGY, Knipe et al. (eds.), 4th ed.,Lippincott-Raven, Philadelphia, (2001)); Influenza viruses such asInfluenza A, B, and C viruses, (see, e.g., Steinhauer et al., Annu RevGenet., 36:305-332 (2002); and Neumann et al., J Gen Virol.,83:2635-2662 (2002)); Hepatitis viruses (see, e.g., Hamasaki et al.,FEBS Lett., 543:51 (2003); Yokota et al., EMBO Rep., 4:602 (2003);Schlomai et al., Hepatology, 37:764 (2003); Wilson et al., Proc. Natl.Acad. Sci. USA, 100:2783 (2003); Kapadia et al., Proc. Natl. Acad. Sci.USA, 100:2014 (2003); and FIELDS VIROLOGY, Knipe et al. (eds.), 4th ed.,Lippincott-Raven, Philadelphia (2001)); Human Immunodeficiency Virus(HIV) (Banerjea et al., Mol. Ther., 8:62 (2003); Song et al., J. Virol.,77:7174 (2003); Stephenson, JAMA, 289:1494 (2003); Qin et al., Proc.Natl. Acad. Sci. USA, 100:183 (2003)); Herpes viruses (Jia et al., J.Virol., 77:3301 (2003)); and Human Papilloma Viruses (HPV) (Hall et al.,J. Virol., 77:6066 (2003); Jiang et al., Oncogene, 21:6041 (2002)).

Exemplary Filovirus nucleic acid sequences that can be silenced include,but are not limited to, nucleic acid sequences encoding structuralproteins (e.g., VP30, VP35, nucleoprotein (NP), polymerase protein(L-pol)) and membrane-associated proteins (e.g., VP40, glycoprotein(GP), VP24). Complete genome sequences for Ebola virus are set forth in,e.g., Genbank Accession Nos. NC_(—)002549; AY769362; NC_(—)006432;NC_(—)004161; AY729654; AY354458; AY142960; AB050936; AF522874;AF499101; AF272001; and AF086833. Ebola virus VP24 sequences are setforth in, e.g., Genbank Accession Nos. U77385 and AY058897. Ebola virusL-pol sequences are set forth in, e.g., Genbank Accession No. X67110.Ebola virus VP40 sequences are set forth in, e.g., Genbank Accession No.AY058896. Ebola virus NP sequences are set forth in, e.g., GenbankAccession No. AY058895. Ebola virus GP sequences are set forth in, e.g.,Genbank Accession No. AY058898; Sanchez et al., Virus Res., 29:215-240(1993); Will et al., J. Virol., 67:1203-1210 (1993); Volchkov et al.,FEBS Lett., 305:181-184 (1992); and U.S. Pat. No. 6,713,069. AdditionalEbola virus sequences are set forth in, e.g., Genbank Accession Nos.L11365 and X61274. Complete genome sequences for Marburg virus are setforth in, e.g., Genbank Accession Nos. NC_(—)001608; AY430365; AY430366;and AY358025. Marburg virus GP sequences are set forth in, e.g., GenbankAccession Nos. AF005734; AF005733; and AF005732. Marburg virus VP35sequences are set forth in, e.g., Genbank Accession Nos. AF005731 andAF005730. Additional Marburg virus sequences are set forth in, e.g.,Genbank Accession Nos. X64406; Z29337; AF005735; and Z12132.Non-limiting examples of siRNA molecules targeting Ebola virus andMarburg virus nucleic acid sequences include those described in U.S.Patent Publication No. 20070135370, the disclosure of which is hereinincorporated by reference in its entirety for all purposes.

Exemplary Influenza virus nucleic acid sequences that can be silencedinclude, but are not limited to, nucleic acid sequences encodingnucleoprotein (NP), matrix proteins (M1 and M2), nonstructural proteins(NS1 and NS2), RNA polymerase (PA, PB1, PB2), neuraminidase (NA), andhaemagglutinin (HA). Influenza A NP sequences are set forth in, e.g.,Genbank Accession Nos. NC_(—)004522; AY818138; AB166863; AB188817;AB189046; AB189054; AB189062; AY646169; AY646177; AY651486; AY651493;AY651494; AY651495; AY651496; AY651497; AY651498; AY651499; AY651500;AY651501; AY651502; AY651503; AY651504; AY651505; AY651506; AY651507;AY651509; AY651528; AY770996; AY790308; AY818138; and AY818140.Influenza A PA sequences are set forth in, e.g., Genbank Accession Nos.AY818132; AY790280; AY646171; AY818132; AY818133; AY646179; AY818134;AY551934; AY651613; AY651610; AY651620; AY651617; AY651600; AY651611;AY651606; AY651618; AY651608; AY651607; AY651605; AY651609; AY651615;AY651616; AY651640; AY651614; AY651612; AY651621; AY651619; AY770995;and AY724786. Non-limiting examples of siRNA molecules targetingInfluenza virus nucleic acid sequences include those described in U.S.Patent Publication No. 20070218122, the disclosure of which is hereinincorporated by reference in its entirety for all purposes.

Exemplary hepatitis virus nucleic acid sequences that can be silencedinclude, but are not limited to, nucleic acid sequences involved intranscription and translation (e.g., En1, En2, X, P) and nucleic acidsequences encoding structural proteins (e.g., core proteins including Cand C-related proteins, capsid and envelope proteins including S, M,and/or L proteins, or fragments thereof) (see, e.g., FIELDS VIROLOGY,supra). Exemplary Hepatitis C virus (HCV) nucleic acid sequences thatcan be silenced include, but are not limited to, the 5′-untranslatedregion (5′-UTR), the 3′-untranslated region (3′-UTR), the polyproteintranslation initiation codon region, the internal ribosome entry site(IRES) sequence, and/or nucleic acid sequences encoding the coreprotein, the E1 protein, the E2 protein, the p7 protein, the NS2protein, the NS3 protease/helicase, the NS4A protein, the NS4B protein,the NS5A protein, and/or the NS5B RNA-dependent RNA polymerase. HCVgenome sequences are set forth in, e.g., Genbank Accession Nos.NC_(—)004102 (HCV genotype 1a), AJ238799 (HCV genotype 1b), NC_(—)009823(HCV genotype 2), NC_(—)009824 (HCV genotype 3), NC_(—)009825 (HCVgenotype 4), NC_(—)009826 (HCV genotype 5), and NC_(—)009827 (HCVgenotype 6). Hepatitis A virus nucleic acid sequences are set forth in,e.g., Genbank Accession No. NC_(—)001489; Hepatitis B virus nucleic acidsequences are set forth in, e.g., Genbank Accession No. NC_(—)003977;Hepatitis D virus nucleic acid sequence are set forth in, e.g., GenbankAccession No. NC_(—)001653; Hepatitis E virus nucleic acid sequences areset forth in, e.g., Genbank Accession No. NC_(—)001434; and Hepatitis Gvirus nucleic acid sequences are set forth in, e.g., Genbank AccessionNo. NC_(—)001710. Silencing of sequences that encode genes associatedwith viral infection and survival can conveniently be used incombination with the administration of conventional agents used to treatthe viral condition. Non-limiting examples of siRNA molecules targetinghepatitis virus nucleic acid sequences include those described in U.S.Patent Publication Nos. 20060281175, 20050058982, and 20070149470; U.S.Pat. No. 7,348,314; and U.S. Provisional Application No. 61/162,127,filed Mar. 20, 2009, the disclosures of which are herein incorporated byreference in their entirety for all purposes.

Genes associated with metabolic diseases and disorders (e.g., disordersin which the liver is the target and liver diseases and disorders)include, for example, genes expressed in dyslipidemia (e.g., liver Xreceptors such as LXRα and LXRβ (Genback Accession No. NM_(—)007121),farnesoid X receptors (FXR) (Genbank Accession No. NM_(—)005123),sterol-regulatory element binding protein (SREBP), site-1 protease(SIP), 3-hydroxy-3-methylglutaryl coenzyme-A reductase (HMG coenzyme-Areductase), apolipoprotein B (ApoB) (Genbank Accession No.NM_(—)000384), apolipoprotein CIII (ApoC3) (Genbank Accession Nos.NM_(—)000040 and NG_(—)008949 REGION: 5001.8164), and apolipoprotein E(ApoE) (Genbank Accession Nos. NM_(—)000041 and NG_(—)007084 REGION:5001.8612)); and diabetes (e.g., glucose 6-phosphatase) (see, e.g.,Forman et al., Cell, 81:687 (1995); Seol et al., Mol. Endocrinol., 9:72(1995), Zavacki et al., Proc. Natl. Acad. Sci. USA, 94:7909 (1997);Sakai et al., Cell, 85:1037-1046 (1996); Duncan et al., J. Biol. Chem.,272:12778-12785 (1997); Willy et al., Genes Dev., 9:1033-1045 (1995);Lehmann et al., J. Biol. Chem., 272:3137-3140 (1997); Janowski et al.,Nature, 383:728-731 (1996); and Peet et al., Cell, 93:693-704 (1998)).One of skill in the art will appreciate that genes associated withmetabolic diseases and disorders (e.g., diseases and disorders in whichthe liver is a target and liver diseases and disorders) include genesthat are expressed in the liver itself as well as and genes expressed inother organs and tissues. Silencing of sequences that encode genesassociated with metabolic diseases and disorders can conveniently beused in combination with the administration of conventional agents usedto treat the disease or disorder. Non-limiting examples of siRNAmolecules targeting the ApoB gene include those described in U.S. PatentPublication No. 20060134189, the disclosure of which is hereinincorporated by reference in its entirety for all purposes. Non-limitingexamples of siRNA molecules targeting the ApoC3 gene include thosedescribed in U.S. Provisional Application No. 61/147,235, filed Jan. 26,2009, the disclosure of which is herein incorporated by reference in itsentirety for all purposes.

Examples of gene sequences associated with tumorigenesis and celltransformation (e.g., cancer or other neoplasia) include mitotickinesins such as Eg5 (KSP, KIF11; Genbank Accession No. NM_(—)004523);serine/threonine kinases such as polo-like kinase 1 (PLK-1) (GenbankAccession No. NM_(—)005030; Barr et al., Nat. Rev. Mol. Cell. Biol.,5:429-440 (2004)); tyrosine kinases such as WEE1 (Genbank Accession Nos.NM_(—)003390 and NM_(—)001143976); inhibitors of apoptosis such as XIAP(Genbank Accession No. NM_(—)001167); COP9 signalosome subunits such asCSN1, CSN2, CSN3, CSN4, CSN5 (JAB1; Genbank Accession No. NM_(—)006837);CSN6, CSN7A, CSN7B, and CSN8; ubiquitin ligases such as COP1 (RFWD2;Genbank Accession Nos. NM_(—)022457 and NM_(—)001001740); and histonedeacetylases such as HDAC1, HDAC2 (Genbank Accession No. NM_(—)001527),HDAC3, HDAC4, HDAC5, HDAC6, HDAC7, HDAC8, HDAC9, etc. Non-limitingexamples of siRNA molecules targeting the Eg5 and XIAP genes includethose described in U.S. patent application Ser. No. 11/807,872, filedMay 29, 2007, the disclosure of which is herein incorporated byreference in its entirety for all purposes. Non-limiting examples ofsiRNA molecules targeting the PLK-1 gene include those described in U.S.Patent Publication Nos. 20050107316 and 20070265438; and U.S. patentapplication Ser. No. 12/343,342, filed Dec. 23, 2008, the disclosures ofwhich are herein incorporated by reference in their entirety for allpurposes. Non-limiting examples of siRNA molecules targeting the CSN5gene include those described in U.S. Provisional Application No.61/045,251, filed Apr. 15, 2008, the disclosure of which is hereinincorporated by reference in its entirety for all purposes.

Additional examples of gene sequences associated with tumorigenesis andcell transformation include translocation sequences such as MLL fusiongenes, BCR-ABL (Wilda et al., Oncogene, 21:5716 (2002); Scherr et al.,Blood, 101:1566 (2003)), TEL-AML1, EWS-FLI1, TLS-FUS, PAX3-FKHR, BCL-2,AML1-ETO, and AML1-MTG8 (Heidenreich et al., Blood, 101:3157 (2003));overexpressed sequences such as multidrug resistance genes (Nieth etal., FEBS Lett., 545:144 (2003); Wu et al, Cancer Res. 63:1515 (2003)),cyclins (Li et al., Cancer Res., 63:3593 (2003); Zou et al., Genes Dev.,16:2923 (2002)), beta-catenin (Verma et al., Clin Cancer Res., 9:1291(2003)), telomerase genes (Kosciolek et al., Mol Cancer Ther., 2:209(2003)), c-MYC, N-MYC, BCL-2, growth factor receptors (e.g., EGFR/ErbB1(Genbank Accession Nos. NM_(—)005228, NM_(—)201282, NM_(—)201283, andNM_(—)201284; see also, Nagy et al. Exp. Cell Res., 285:39-49 (2003),ErbB2/HER-2 (Genbank Accession Nos. NM_(—)004448 and NM_(—)001005862),ErbB3 (Genbank Accession Nos. NM_(—)001982 and NM_(—)001005915), andErbB4 (Genbank Accession Nos. NM_(—)005235 and NM_(—)001042599); andmutated sequences such as RAS (reviewed in Tuschl and Borkhardt, Mol.Interventions, 2:158 (2002)). Non-limiting examples of siRNA moleculestargeting the EGFR gene include those described in U.S. patentapplication Ser. No. 11/807,872, filed May 29, 2007, the disclosure ofwhich is herein incorporated by reference in its entirety for allpurposes.

Silencing of sequences that encode DNA repair enzymes find use incombination with the administration of chemotherapeutic agents (Colliset al., Cancer Res., 63:1550 (2003)). Genes encoding proteins associatedwith tumor migration are also target sequences of interest, for example,integrins, selectins, and metalloproteinases. The foregoing examples arenot exclusive. Those of skill in the art will understand that any wholeor partial gene sequence that facilitates or promotes tumorigenesis orcell transformation, tumor growth, or tumor migration can be included asa template sequence.

Angiogenic genes are able to promote the formation of new vessels. Ofparticular interest is vascular endothelial growth factor (VEGF) (Reichet al., Mol. Vis., 9:210 (2003)) or VEGFR. siRNA sequences that targetVEGFR are set forth in, e.g., GB 2396864; U.S. Patent Publication No.20040142895; and CA 2456444, the disclosures of which are hereinincorporated by reference in their entirety for all purposes.

Anti-angiogenic genes are able to inhibit neovascularization. Thesegenes are particularly useful for treating those cancers in whichangiogenesis plays a role in the pathological development of thedisease. Examples of anti-angiogenic genes include, but are not limitedto, endostatin (see, e.g., U.S. Pat. No. 6,174,861), angiostatin (see,e.g., U U.S. Pat. No. 5,639,725), and VEGFR2 (see, e.g., Decaussin etal., J. Pathol., 188: 369-377 (1999)), the disclosures of which areherein incorporated by reference in their entirety for all purposes.

Immunomodulator genes are genes that modulate one or more immuneresponses. Examples of immunomodulator genes include, withoutlimitation, cytokines such as growth factors (e.g., TGF-α, TGF-β, EGF,FGF, IGF, NGF, PDGF, CGF, GM-CSF, SCF, etc.), interleukins (e.g., IL-2,IL-4, IL-12 (Hill et al., J. Immunol., 171:691 (2003)), IL-15, IL-18,IL-20, etc.), interferons (e.g., IFN-α, IFN-β, IFN-γ, etc.) and TNF. Fasand Fas ligand genes are also immunomodulator target sequences ofinterest (Song et al., Nat. Med., 9:347 (2003)). Genes encodingsecondary signaling molecules in hematopoietic and lymphoid cells arealso included in the present invention, for example, Tec family kinasessuch as Bruton's tyrosine kinase (Btk) (Heinonen et al., FEBS Lett.,527:274 (2002)).

Cell receptor ligands include ligands that are able to bind to cellsurface receptors (e.g., insulin receptor, EPO receptor, G-proteincoupled receptors, receptors with tyrosine kinase activity, cytokinereceptors, growth factor receptors, etc.), to modulate (e.g., inhibit,activate, etc.) the physiological pathway that the receptor is involvedin (e.g., glucose level modulation, blood cell development, mitogenesis,etc.). Examples of cell receptor ligands include, but are not limitedto, cytokines, growth factors, interleukins, interferons, erythropoietin(EPO), insulin, glucagon, G-protein coupled receptor ligands, etc.Templates coding for an expansion of trinucleotide repeats (e.g., CAGrepeats) find use in silencing pathogenic sequences in neurodegenerativedisorders caused by the expansion of trinucleotide repeats, such asspinobulbular muscular atrophy and Huntington's Disease (Caplen et al.,Hum. Mol. Genet., 11:175 (2002)).

In addition to its utility in silencing the expression of any of theabove-described genes for therapeutic purposes, the siRNA describedherein are also useful in research and development applications as wellas diagnostic, prophylactic, prognostic, clinical, and other healthcareapplications. As a non-limiting example, the siRNA can be used in targetvalidation studies directed at testing whether a gene of interest hasthe potential to be a therapeutic target. The siRNA can also be used intarget identification studies aimed at discovering genes as potentialtherapeutic targets.

2. aiRNA

Like siRNA, asymmetrical interfering RNA (aiRNA) can recruit theRNA-induced silencing complex (RISC) and lead to effective silencing ofa variety of genes in mammalian cells by mediating sequence-specificcleavage of the target sequence between nucleotide 10 and 11 relative tothe 5′ end of the antisense strand (Sun et al., Nat. Biotech.,26:1379-1382 (2008)). Typically, an aiRNA molecule comprises a short RNAduplex having a sense strand and an antisense strand, wherein the duplexcontains overhangs at the 3′ and 5′ ends of the antisense strand. TheaiRNA is generally asymmetric because the sense strand is shorter onboth ends when compared to the complementary antisense strand. In someaspects, aiRNA molecules may be designed, synthesized, and annealedunder conditions similar to those used for siRNA molecules. As anon-limiting example, aiRNA sequences may be selected and generatedusing the methods described above for selecting siRNA sequences.

In another embodiment, aiRNA duplexes of various lengths (e.g., about10-25, 12-20, 12-19, 12-18, 13-17, or 14-17 base pairs, more typically12, 13, 14, 15, 16, 17, 18, 19, or base pairs) may be designed withoverhangs at the 3′ and 5′ ends of the antisense strand to target anmRNA of interest. In certain instances, the sense strand of the aiRNAmolecule is about 10-25, 12-20, 12-19, 12-18, 13-17, or 14-17nucleotides in length, more typically 12, 13, 14, 15, 16, 17, 18, 19, or20 nucleotides in length. In certain other instances, the antisensestrand of the aiRNA molecule is about 15-60, 15-50, or 15-40 nucleotidesin length, more typically about 15-30, 15-25, or 19-25 nucleotides inlength, and is preferably about 20-24, 21-22, or 21-23 nucleotides inlength.

In some embodiments, the 5′ antisense overhang contains one, two, three,four, or more nontargeting nucleotides (e.g., “AA”, “UU”, “dTdT”, etc.).In other embodiments, the 3′ antisense overhang contains one, two,three, four, or more nontargeting nucleotides (e.g., “AA”, “UU”, “dTdT”,etc.). In certain aspects, the aiRNA molecules described herein maycomprise one or more modified nucleotides, e.g., in the double-stranded(duplex) region and/or in the antisense overhangs. As a non-limitingexample, aiRNA sequences may comprise one or more of the modifiednucleotides described above for siRNA sequences. In a preferredembodiment, the aiRNA molecule comprises 2′OMe nucleotides such as, forexample, 2′OMe-guanosine nucleotides, 2′OMe-uridine nucleotides, ormixtures thereof.

In certain embodiments, aiRNA molecules may comprise an antisense strandwhich corresponds to the antisense strand of an siRNA molecule, e.g.,one of the siRNA molecules described herein. In other embodiments, aiRNAmolecules may be used to silence the expression of any of the targetgenes set forth above, such as, e.g., genes associated with viralinfection and survival, genes associated with metabolic diseases anddisorders, genes associated with tumorigenesis and cell transformation,angiogenic genes, immunomodulator genes such as those associated withinflammatory and autoimmune responses, ligand receptor genes, and genesassociated with neurodegenerative disorders.

3. miRNA

Generally, microRNAs (miRNA) are single-stranded RNA molecules of about21-23 nucleotides in length which regulate gene expression. miRNAs areencoded by genes from whose DNA they are transcribed, but miRNAs are nottranslated into protein (non-coding RNA); instead, each primarytranscript (a pri-miRNA) is processed into a short stem-loop structurecalled a pre-miRNA and finally into a functional mature miRNA. MaturemiRNA molecules are either partially or completely complementary to oneor more messenger RNA (mRNA) molecules, and their main function is todownregulate gene expression. The identification of miRNA molecules isdescribed, e.g., in Lagos-Quintana et al., Science, 294:853-858; Lau etal., Science, 294:858-862; and Lee et al., Science, 294:862-864.

The genes encoding miRNA are much longer than the processed mature miRNAmolecule. miRNA are first transcribed as primary transcripts orpri-miRNA with a cap and poly-A tail and processed to short,˜70-nucleotide stem-loop structures known as pre-miRNA in the cellnucleus. This processing is performed in animals by a protein complexknown as the Microprocessor complex, consisting of the nuclease Droshaand the double-stranded RNA binding protein Pasha (Denli et al., Nature,432:231-235 (2004)). These pre-miRNA are then processed to mature miRNAin the cytoplasm by interaction with the endonuclease Dicer, which alsoinitiates the formation of the RNA-induced silencing complex (RISC)(Bernstein et al., Nature, 409:363-366 (2001). Either the sense strandor antisense strand of DNA can function as templates to give rise tomiRNA.

When Dicer cleaves the pre-miRNA stem-loop, two complementary short RNAmolecules are formed, but only one is integrated into the RISC complex.This strand is known as the guide strand and is selected by theargonaute protein, the catalytically active RNase in the RISC complex,on the basis of the stability of the 5′ end (Preall et al., Curr. Biol.,16:530-535 (2006)). The remaining strand, known as the anti-guide orpassenger strand, is degraded as a RISC complex substrate (Gregory etal., Cell, 123:631-640 (2005)). After integration into the active RISCcomplex, miRNAs base pair with their complementary mRNA molecules andinduce target mRNA degradation and/or translational silencing.

Mammalian miRNA molecules are usually complementary to a site in the 3′UTR of the target mRNA sequence. In certain instances, the annealing ofthe miRNA to the target mRNA inhibits protein translation by blockingthe protein translation machinery. In certain other instances, theannealing of the miRNA to the target mRNA facilitates the cleavage anddegradation of the target mRNA through a process similar to RNAinterference (RNAi). miRNA may also target methylation of genomic siteswhich correspond to targeted mRNA. Generally, miRNA function inassociation with a complement of proteins collectively termed the miRNP.

In certain aspects, the miRNA molecules described herein are about15-100, 15-90, 15-80, 15-75, 15-70, 15-60, 15-50, or 15-40 nucleotidesin length, more typically about 15-30, 15-25, or 19-25 nucleotides inlength, and are preferably about 20-24, 21-22, or 21-23 nucleotides inlength. In certain other aspects, miRNA molecules may comprise one ormore modified nucleotides. As a non-limiting example, miRNA sequencesmay comprise one or more of the modified nucleotides described above forsiRNA sequences. In a preferred embodiment, the miRNA molecule comprises2′OMe nucleotides such as, for example, 2′OMe-guanosine nucleotides,2′OMe-uridine nucleotides, or mixtures thereof.

In some embodiments, miRNA molecules may be used to silence theexpression of any of the target genes set forth above, such as, e.g.,genes associated with viral infection and survival, genes associatedwith metabolic diseases and disorders, genes associated withtumorigenesis and cell transformation, angiogenic genes, immunomodulatorgenes such as those associated with inflammatory and autoimmuneresponses, ligand receptor genes, and genes associated withneurodegenerative disorders.

In other embodiments, one or more agents that block the activity of amiRNA targeting an mRNA of interest are administered using a lipidparticle of the invention (e.g., a nucleic acid-lipid particle).Examples of blocking agents include, but are not limited to, stericblocking oligonucleotides, locked nucleic acid oligonucleotides, andMorpholino oligonucleotides. Such blocking agents may bind directly tothe miRNA or to the miRNA binding site on the target mRNA.

4. Antisense Oligonucleotides

In one embodiment, the nucleic acid is an antisense oligonucleotidedirected to a target gene or sequence of interest. The terms “antisenseoligonucleotide” or “antisense” include oligonucleotides that arecomplementary to a targeted polynucleotide sequence. Antisenseoligonucleotides are single strands of DNA or RNA that are complementaryto a chosen sequence. Antisense RNA oligonucleotides prevent thetranslation of complementary RNA strands by binding to the RNA.Antisense DNA oligonucleotides can be used to target a specific,complementary (coding or non-coding) RNA. If binding occurs, thisDNA/RNA hybrid can be degraded by the enzyme RNase H. In a particularembodiment, antisense oligonucleotides comprise from about 10 to about60 nucleotides, more preferably from about 15 to about 30 nucleotides.The term also encompasses antisense oligonucleotides that may not beexactly complementary to the desired target gene. Thus, the inventioncan be utilized in instances where non-target specific-activities arefound with antisense, or where an antisense sequence containing one ormore mismatches with the target sequence is the most preferred for aparticular use.

Antisense oligonucleotides have been demonstrated to be effective andtargeted inhibitors of protein synthesis, and, consequently, can be usedto specifically inhibit protein synthesis by a targeted gene. Theefficacy of antisense oligonucleotides for inhibiting protein synthesisis well established. For example, the synthesis of polygalactauronaseand the muscarine type 2 acetylcholine receptor are inhibited byantisense oligonucleotides directed to their respective mRNA sequences(see, U.S. Pat. Nos. 5,739,119 and 5,759,829). Furthermore, examples ofantisense inhibition have been demonstrated with the nuclear proteincyclin, the multiple drug resistance gene (MDR1), ICAM-1, E-selectin,STK-1, striatal GABAA receptor, and human EGF (see, Jaskulski et al.,Science, 240:1544-6 (1988); Vasanthakumar et al., Cancer Commun.,1:225-32 (1989); Penis et al., Brain Res Mol Brain Res., 15; 57:310-20(1998); and U.S. Pat. Nos. 5,801,154; 5,789,573; 5,718,709 and5,610,288). Moreover, antisense constructs have also been described thatinhibit and can be used to treat a variety of abnormal cellularproliferations, e.g., cancer (see, U.S. Pat. Nos. 5,747,470; 5,591,317;and 5,783,683). The disclosures of these references are hereinincorporated by reference in their entirety for all purposes.

Methods of producing antisense oligonucleotides are known in the art andcan be readily adapted to produce an antisense oligonucleotide thattargets any polynucleotide sequence. Selection of antisenseoligonucleotide sequences specific for a given target sequence is basedupon analysis of the chosen target sequence and determination ofsecondary structure, T_(m), binding energy, and relative stability.Antisense oligonucleotides may be selected based upon their relativeinability to form dimers, hairpins, or other secondary structures thatwould reduce or prohibit specific binding to the target mRNA in a hostcell. Highly preferred target regions of the mRNA include those regionsat or near the AUG translation initiation codon and those sequences thatare substantially complementary to 5′ regions of the mRNA. Thesesecondary structure analyses and target site selection considerationscan be performed, for example, using v.4 of the OLIGO primer analysissoftware (Molecular Biology Insights) and/or the BLASTN 2.0.5 algorithmsoftware (Altschul et al., Nucleic Acids Res., 25:3389-402 (1997)).

5. Ribozymes

According to another embodiment of the invention, nucleic acid-lipidparticles are associated with ribozymes. Ribozymes are RNA-proteincomplexes having specific catalytic domains that possess endonucleaseactivity (see, Kim et al., Proc. Natl. Acad. Sci. USA., 84:8788-92(1987); and Forster et al., Cell, 49:211-20 (1987)). For example, alarge number of ribozymes accelerate phosphoester transfer reactionswith a high degree of specificity, often cleaving only one of severalphosphoesters in an oligonucleotide substrate (see, Cech et al., Cell,27:487-96 (1981); Michel et al., J. Mol. Biol., 216:585-610 (1990);Reinhold-Hurek et al., Nature, 357:173-6 (1992)). This specificity hasbeen attributed to the requirement that the substrate bind via specificbase-pairing interactions to the internal guide sequence (“IGS”) of theribozyme prior to chemical reaction.

At least six basic varieties of naturally-occurring enzymatic RNAmolecules are known presently. Each can catalyze the hydrolysis of RNAphosphodiester bonds in trans (and thus can cleave other RNA molecules)under physiological conditions. In general, enzymatic nucleic acids actby first binding to a target RNA. Such binding occurs through the targetbinding portion of an enzymatic nucleic acid which is held in closeproximity to an enzymatic portion of the molecule that acts to cleavethe target RNA. Thus, the enzymatic nucleic acid first recognizes andthen binds a target RNA through complementary base-pairing, and oncebound to the correct site, acts enzymatically to cut the target RNA.Strategic cleavage of such a target RNA will destroy its ability todirect synthesis of an encoded protein. After an enzymatic nucleic acidhas bound and cleaved its RNA target, it is released from that RNA tosearch for another target and can repeatedly bind and cleave newtargets.

The enzymatic nucleic acid molecule may be formed in a hammerhead,hairpin, hepatitis δ virus, group I intron or RNaseP RNA (in associationwith an RNA guide sequence), or Neurospora VS RNA motif, for example.Specific examples of hammerhead motifs are described in, e.g., Rossi etal., Nucleic Acids Res., 20:4559-65 (1992). Examples of hairpin motifsare described in, e.g., EP 0360257, Hampel et al., Biochemistry,28:4929-33 (1989); Hampel et al., Nucleic Acids Res., 18:299-304 (1990);and U.S. Pat. No. 5,631,359. An example of the hepatitis δ virus motifis described in, e.g., Perrotta et al., Biochemistry, 31:11843-52(1992). An example of the RNaseP motif is described in, e.g.,Guerrier-Takada et al., Cell, 35:849-57 (1983). Examples of theNeurospora VS RNA ribozyme motif is described in, e.g., Saville et al.,Cell, 61:685-96 (1990); Saville et al., Proc. Natl. Acad. Sci. USA,88:8826-30 (1991); Collins et al., Biochemistry, 32:2795-9 (1993). Anexample of the Group I intron is described in, e.g., U.S. Pat. No.4,987,071. Important characteristics of enzymatic nucleic acid moleculesused according to the invention are that they have a specific substratebinding site which is complementary to one or more of the target geneDNA or RNA regions, and that they have nucleotide sequences within orsurrounding that substrate binding site which impart an RNA cleavingactivity to the molecule. Thus, the ribozyme constructs need not belimited to specific motifs mentioned herein. The disclosures of thesereferences are herein incorporated by reference in their entirety forall purposes.

Methods of producing a ribozyme targeted to any polynucleotide sequenceare known in the art. Ribozymes may be designed as described in, e.g.,PCT Publication Nos. WO 93/23569 and WO 94/02595, and synthesized to betested in vitro and/or in vivo as described therein. The disclosures ofthese PCT publications are herein incorporated by reference in theirentirety for all purposes.

Ribozyme activity can be optimized by altering the length of theribozyme binding arms or chemically synthesizing ribozymes withmodifications that prevent their degradation by serum ribonucleases(see, e.g., PCT Publication Nos. WO 92/07065, WO 93/15187, WO 91/03162,and WO 94/13688; EP 92110298.4; and U.S. Pat. No. 5,334,711, whichdescribe various chemical modifications that can be made to the sugarmoieties of enzymatic RNA molecules, the disclosures of which are eachherein incorporated by reference in their entirety for all purposes),modifications which enhance their efficacy in cells, and removal of stemII bases to shorten RNA synthesis times and reduce chemicalrequirements.

6. Immunostimulatory Oligonucleotides

Nucleic acids associated with lipid particles of the present inventionmay be immunostimulatory, including immunostimulatory oligonucleotides(ISS; single- or double-stranded) capable of inducing an immune responsewhen administered to a subject, which may be a mammal such as a human.ISS include, e.g., certain palindromes leading to hairpin secondarystructures (see, Yamamoto et al., J. Immunol., 148:4072-6 (1992)), orCpG motifs, as well as other known ISS features (such as multi-Gdomains; see; PCT Publication No. WO 96/11266, the disclosure of whichis herein incorporated by reference in its entirety for all purposes).

Immunostimulatory nucleic acids are considered to be non-sequencespecific when it is not required that they specifically bind to andreduce the expression of a target sequence in order to provoke an immuneresponse. Thus, certain immunostimulatory nucleic acids may comprise asequence corresponding to a region of a naturally-occurring gene ormRNA, but they may still be considered non-sequence specificimmunostimulatory nucleic acids.

In one embodiment, the immunostimulatory nucleic acid or oligonucleotidecomprises at least one CpG dinucleotide. The oligonucleotide or CpGdinucleotide may be unmethylated or methylated. In another embodiment,the immunostimulatory nucleic acid comprises at least one CpGdinucleotide having a methylated cytosine. In one embodiment, thenucleic acid comprises a single CpG dinucleotide, wherein the cytosinein the CpG dinucleotide is methylated. In an alternative embodiment, thenucleic acid comprises at least two CpG dinucleotides, wherein at leastone cytosine in the CpG dinucleotides is methylated. In a furtherembodiment, each cytosine in the CpG dinucleotides present in thesequence is methylated. In another embodiment, the nucleic acidcomprises a plurality of CpG dinucleotides, wherein at least one of theCpG dinucleotides comprises a methylated cytosine. Examples ofimmunostimulatory oligonucleotides suitable for use in the compositionsand methods of the present invention are described in PCT ApplicationNo. PCT/US08/88676, filed Dec. 31, 2008, PCT Publication Nos. WO02/069369 and WO 01/15726, U.S. Pat. No. 6,406,705, and Raney et al., J.Pharm. Exper. Ther., 298:1185-92 (2001), the disclosures of which areeach herein incorporated by reference in their entirety for allpurposes. In certain embodiments, the oligonucleotides used in thecompositions and methods of the invention have a phosphodiester (“PO”)backbone or a phosphorothioate (“PS”) backbone, and/or at least onemethylated cytosine residue in a CpG motif.

B. Other Active Agents

In certain embodiments, the active agent associated with the lipidparticles of the invention may comprise one or more therapeuticproteins, polypeptides, or small organic molecules or compounds.Non-limiting examples of such therapeutically effective agents or drugsinclude oncology drugs (e.g., chemotherapy drugs, hormonal therapeuticagents, immunotherapeutic agents, radiotherapeutic agents, etc.),lipid-lowering agents, anti-viral drugs, anti-inflammatory compounds,antidepressants, stimulants, analgesics, antibiotics, birth controlmedication, antipyretics, vasodilators, anti-angiogenics, cytovascularagents, signal transduction inhibitors, cardiovascular drugs such asanti-arrhythmic agents, hormones, vasoconstrictors, and steroids. Theseactive agents may be administered alone in the lipid particles of theinvention, or in combination (e.g., co-administered) with lipidparticles of the invention comprising nucleic acid such as interferingRNA.

Non-limiting examples of chemotherapy drugs include platinum-based drugs(e.g., oxaliplatin, cisplatin, carboplatin, spiroplatin, iproplatin,satraplatin, etc.), alkylating agents (e.g., cyclophosphamide,ifosfamide, chlorambucil, busulfan, melphalan, mechlorethamine,uramustine, thiotepa, nitrosoureas, etc.), anti-metabolites (e.g.,5-fluorouracil (5-FU), azathioprine, methotrexate, leucovorin,capecitabine, cytarabine, floxuridine, fludarabine, gemcitabine,pemetrexed, raltitrexed, etc.), plant alkaloids (e.g., vincristine,vinblastine, vinorelbine, vindesine, podophyllotoxin, paclitaxel(taxol), docetaxel, etc.), topoisomerase inhibitors (e.g., irinotecan(CPT-11; Camptosar), topotecan, amsacrine, etoposide (VP16), etoposidephosphate, teniposide, etc.), antitumor antibiotics (e.g., doxorubicin,adriamycin, daunorubicin, epirubicin, actinomycin, bleomycin, mitomycin,mitoxantrone, plicamycin, etc.), tyrosine kinase inhibitors (e.g.,gefltinib (Iressa®), sunitinib (Sutent®; SU11248), erlotinib (Tarceva®;OSI-1774), lapatinib (GW572016; GW2016), canertinib (CI 1033), semaxinib(SU5416), vatalanib (PTK787/ZK222584), sorafenib (BAY 43-9006), imatinib(Gleevec®; STI571), dasatinib (BMS-354825), leflunomide (SU101),vandetanib (Zactima™; ZD6474), etc.), pharmaceutically acceptable saltsthereof, stereoisomers thereof, derivatives thereof, analogs thereof,and combinations thereof.

Examples of conventional hormonal therapeutic agents include, withoutlimitation, steroids (e.g., dexamethasone), finasteride, aromataseinhibitors, tamoxifen, and goserelin as well as othergonadotropin-releasing hormone agonists (GnRH).

Examples of conventional immunotherapeutic agents include, but are notlimited to, immunostimulants (e.g., Bacillus Calmette-Guérin (BCG),levamisole, interleukin-2, alpha-interferon, etc.), monoclonalantibodies (e.g., anti-CD20, anti-HER2, anti-CD52, anti-HLA-DR, andanti-VEGF monoclonal antibodies), immunotoxins (e.g., anti-CD33monoclonal antibody-calicheamicin conjugate, anti-CD22 monoclonalantibody-pseudomonas exotoxin conjugate, etc.), and radioimmunotherapy(e.g., anti-CD20 monoclonal antibody conjugated to ¹¹¹In, ⁹⁰Y, or ¹³¹I,etc.).

Examples of conventional radiotherapeutic agents include, but are notlimited to, radionuclides such as ⁴⁷Sc, ⁶⁴Cu, ⁶⁷Cu, ⁸⁹Sr, ⁸⁶Y, ⁸⁷Y, ⁹⁰Y,¹⁰⁵Rh, ¹¹¹Ag, ¹¹¹In, ^(117m)Sn, ¹⁴⁹Pm, ¹⁵³Sm, ¹⁶⁶Ho, ¹⁷⁷Lu, ¹⁸⁶Re,¹⁸⁸Re, ²¹¹At, and ²¹²Bi, optionally conjugated to antibodies directedagainst tumor antigens.

Additional oncology drugs that may be used according to the inventioninclude, but are not limited to, alkeran, allopurinol, altretamine,amifostine, anastrozole, araC, arsenic trioxide, bexarotene, biCNU,carmustine, CCNU, celecoxib, cladribine, cyclosporin A, cytosinearabinoside, cytoxan, dexrazoxane, DTIC, estramustine, exemestane,FK506, gemtuzumab-ozogamicin, hydrea, hydroxyurea, idarubicin,interferon, letrozole, leustatin, leuprolide, litretinoin, megastrol,L-PAM, mesna, methoxsalen, mithramycin, nitrogen mustard, pamidronate,Pegademase, pentostatin, porfimer sodium, prednisone, rituxan,streptozocin, STI-571, taxotere, temozolamide, VM-26, toremifene,tretinoin, ATRA, valrubicin, and velban. Other examples of oncologydrugs that may be used according to the invention are ellipticin andellipticin analogs or derivatives, epothilones, intracellular kinaseinhibitors, and camptothecins.

Non-limiting examples of lipid-lowering agents for treating a lipiddisease or disorder associated with elevated triglycerides, cholesterol,and/or glucose include statins, fibrates, ezetimibe, thiazolidinediones,niacin, beta-blockers, nitroglycerin, calcium antagonists, fish oil, andmixtures thereof.

Examples of anti-viral drugs include, but are not limited to, abacavir,aciclovir, acyclovir, adefovir, amantadine, amprenavir, arbidol,atazanavir, atripla, cidofovir, combivir, darunavir, delavirdine,didanosine, docosanol, edoxudine, efavirenz, emtricitabine, enfuvirtide,entecavir, entry inhibitors, famciclovir, fixed dose combinations,fomivirsen, fosamprenavir, foscarnet, fosfonet, fusion inhibitors,ganciclovir, ibacitabine, immunovir, idoxuridine, imiquimod, indinavir,inosine, integrase inhibitors, interferon type III (e.g., IFN-λmolecules such as IFN-λ1, IFN-λ2, and IFN-λ3), interferon type II (e.g.,IFN-γ), interferon type I (e.g., IFN-α such as PEGylated IFN-α, IFN-β,IFN-κ, IFN-δ, IFN-ε, IFN-τ, IFN-ω, and IFN-ζ), interferon, lamivudine,lopinavir, loviride, MK-0518, maraviroc, moroxydine, nelfinavir,nevirapine, nexavir, nucleoside analogues, oseltamivir, penciclovir,peramivir, pleconaril, podophyllotoxin, protease inhibitors, reversetranscriptase inhibitors, ribavirin, rimantadine, ritonavir, saquinavir,stavudine, synergistic enhancers, tenofovir, tenofovir disoproxil,tipranavir, trifluridine, trizivir, tromantadine, truvada, valaciclovir,valganciclovir, vicriviroc, vidarabine, viramidine, zalcitabine,zanamivir, zidovudine, pharmaceutically acceptable salts thereof,stereoisomers thereof, derivatives thereof, analogs thereof, andmixtures thereof.

V. Lipid Particles

The lipid particles of the invention typically comprise an active agentor therapeutic agent, a cationic lipid, a non-cationic lipid, and aconjugated lipid that inhibits aggregation of particles. In someembodiments, the active agent or therapeutic agent is fully encapsulatedwithin the lipid portion of the lipid particle such that the activeagent or therapeutic agent in the lipid particle is resistant in aqueoussolution to enzymatic degradation, e.g., by a nuclease or protease. Inother embodiments, the lipid particles described herein aresubstantially non-toxic to mammals such as humans. The lipid particlesof the invention typically have a mean diameter of from about 40 nm toabout 150 nm, from about 50 nm to about 150 nm, from about 60 nm toabout 130 nm, from about 70 nm to about 110 nm, or from about 70 toabout 90 nm.

In preferred embodiments, the lipid particles of the invention areserum-stable nucleic acid-lipid particles (SNALP) which comprise aninterfering RNA (e.g., siRNA, aiRNA, and/or miRNA), a cationic lipid(e.g., a cationic lipid of Formulas I, II, and/or III), a non-cationiclipid (e.g., cholesterol alone or mixtures of one or more phospholipidsand cholesterol), and a conjugated lipid that inhibits aggregation ofthe particles (e.g., one or more PEG-lipid conjugates). The SNALP maycomprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more unmodifiedand/or modified interfering RNA molecules. Nucleic acid-lipid particlesand their method of preparation are described in, e.g., U.S. Pat. Nos.5,753,613; 5,785,992; 5,705,385; 5,976,567; 5,981,501; 6,110,745; and6,320,017; and PCT Publication No. WO 96/40964, the disclosures of whichare each herein incorporated by reference in their entirety for allpurposes.

A. Cationic Lipids

Any of a variety of cationic lipids may be used in the lipid particlesof the invention (e.g., SNALP), either alone or in combination with oneor more other cationic lipid species or non-cationic lipid species.

Cationic lipids which are useful in the present invention can be any ofa number of lipid species which carry a net positive charge atphysiological pH. Such lipids include, but are not limited to,N,N-dioleyl-N,N-dimethylammonium chloride (DODAC),1,2-dioleyloxy-N,N-dimethylaminopropane (DODMA),1,2-distearyloxy-N,N-dimethylaminopropane (DSDMA),N-(1-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA),N,N-distearyl-N,N-dimethylammonium bromide (DDAB),N-(1-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP),3-(N—(N′,N′-dimethylaminoethane)-carbamoyl)cholesterol (DC-Chol),N-(1,2-dimyristyloxyprop-3-yl)-N,N-dimethyl-N-hydroxyethyl ammoniumbromide (DMRIE),2,3-dioleyloxy-N-[2(spermine-carboxamido)ethyl]-N,N-dimethyl-1-propanaminiumtrifluoroacetate(DOSPA), dioctadecylamidoglycyl spermine (DOGS),3-dimethylamino-2-(cholest-5-en-3-beta-oxybutan-4-oxy)-1-(cis,cis-9,12-octadecadienoxy)propane(CLinDMA),2-[5′-(cholest-5-en-3.beta.-oxy)-3′-oxapentoxy)-3-dimethyl-1-(cis,cis-9′,1-2′-octadecadienoxy)propane(CpLinDMA), N,N-dimethyl-3,4-dioleyloxybenzylamine (DMOBA),1,2-N,N′-dioleylcarbamyl-3-dimethylaminopropane (DOcarbDAP),1,2-N,N′-Dilinoleylcarbamyl-3-dimethylaminopropane (DLincarbDAP),1,2-Dilinoleoylcarbamyl-3-dimethylaminopropane (DLinCDAP), and mixturesthereof. A number of these lipids and related analogs have beendescribed in U.S. Patent Publication Nos. 20060083780 and 20060240554;U.S. Pat. Nos. 5,208,036; 5,264,618; 5,279,833; 5,283,185; 5,753,613;and 5,785,992; and PCT Publication No. WO 96/10390, the disclosures ofwhich are each herein incorporated by reference in their entirety forall purposes. Additionally, a number of commercial preparations ofcationic lipids are available and can be used in the present invention.These include, e.g., LIPOFECTIN® (commercially available cationicliposomes comprising DOTMA and DOPE, from GIBCO/BRL, Grand Island, N.Y.,USA); LIPOFECTAMINE® (commercially available cationic liposomescomprising DOSPA and DOPE, from GIBCO/BRL); and TRANSFECTAM®(commercially available cationic liposomes comprising DOGS from PromegaCorp., Madison, Wis., USA).

Additionally, cationic lipids of Formula I having the followingstructures are useful in the present invention.

wherein R¹ and R² are independently selected and are H or C₁-C₃ alkyls,R³ and R⁴ are independently selected and are alkyl groups having fromabout 10 to about 20 carbon atoms, and at least one of R³ and R⁴comprises at least two sites of unsaturation. In certain instances, R³and R⁴ are both the same, i.e., R³ and R⁴ are both linoleyl (C₁₈), etc.In certain other instances, R³ and R⁴ are different, i.e., R³ istetradectrienyl (C₁₄) and R⁴ is linoleyl (C₁₈). In a preferredembodiment, the cationic lipid of Formula I is symmetrical, i.e., R³ andR⁴ are both the same. In another preferred embodiment, both R³ and R⁴comprise at least two sites of unsaturation. In some embodiments, R³ andR⁴ are independently selected from the group consisting of dodecadienyl,tetradecadienyl, hexadecadienyl, linoleyl, and icosadienyl. In apreferred embodiment, R³ and R⁴ are both linoleyl. In some embodiments,R³ and R⁴ comprise at least three sites of unsaturation and areindependently selected from, e.g., dodecatrienyl, tetradectrienyl,hexadecatrienyl, linolenyl, and icosatrienyl. In particularly preferredembodiments, the cationic lipid of Formula I is1,2-dilinoleyloxy-N,N-dimethylaminopropane (DLinDMA) or1,2-dilinolenyloxy-N,N-dimethylaminopropane (DLenDMA).

Furthermore, cationic lipids of Formula II having the followingstructures are useful in the present invention.

wherein R¹ and R² are independently selected and are H or C₁-C₃ alkyls,R³ and R⁴ are independently selected and are alkyl groups having fromabout 10 to about 20 carbon atoms, and at least one of R³ and R⁴comprises at least two sites of unsaturation. In certain instances, R³and R⁴ are both the same, i.e., R³ and R⁴ are both linoleyl (C₁₈), etc.In certain other instances, R³ and R⁴ are different, i.e., R³ istetradectrienyl (C₁₄) and R⁴ is linoleyl (C₁₈). In a preferredembodiment, the cationic lipids of the present invention aresymmetrical, i.e., R³ and R⁴ are both the same. In another preferredembodiment, both R³ and R⁴ comprise at least two sites of unsaturation.In some embodiments, R³ and R⁴ are independently selected from the groupconsisting of dodecadienyl, tetradecadienyl, hexadecadienyl, linoleyl,and icosadienyl. In a preferred embodiment, R³ and R⁴ are both linoleyl.In some embodiments, R³ and R⁴ comprise at least three sites ofunsaturation and are independently selected from, e.g., dodecatrienyl,tetradectrienyl, hexadecatrienyl, linolenyl, and icosatrienyl.

Moreover, cationic lipids of Formula III having the following structures(or salts thereof) are useful in the present invention.

Wherein R¹ and R² are either the same or different and independentlyoptionally substituted C₁₂-C₂₄ alkyl, optionally substituted C₁₂-C₂₄alkenyl, optionally substituted C₁₂-C₂₄ alkynyl, or optionallysubstituted C₁₂-C₂₄ acyl; R³ and R⁴ are either the same or different andindependently optionally substituted C₁-C₆ alkyl, optionally substitutedC₁-C₆ alkenyl, or optionally substituted C₁-C₆ alkynyl or R³ and R⁴ mayjoin to form an optionally substituted heterocyclic ring of 4 to 6carbon atoms and 1 or 2 heteroatoms chosen from nitrogen and oxygen; R⁵is either absent or hydrogen or C₁-C₆ alkyl to provide a quaternaryamine; m, n, and p are either the same or different and independentlyeither 0 or 1 with the proviso that m, n, and p are not simultaneously0; q is 0, 1, 2, 3, or 4; and Y and Z are either the same or differentand independently O, S, or NH.

In some embodiments, the cationic lipid of Formula III is2,2-dilinoleyl-4-(2-dimethylaminoethyl)-[1,3]-dioxolane (DLin-K-C2-DMA;“XTC2”), 2,2-dilinoleyl-4-(3-dimethylaminopropyl)-[1,3]-dioxolane(DLin-K-C3-DMA), 2,2-dilinoleyl-4-(4-dimethylaminobutyl)-[1,3]-dioxolane(DLin-K-C4-DMA), 2,2-dilinoleyl-5-dimethylaminomethyl-[1,3]-dioxane(DLin-K6-DMA), 2,2-dilinoleyl-4-N-methylpepiazino-[1,3]-dioxolane(DLin-K-MPZ), 2,2-dilinoleyl-4-dimethylaminomethyl-[1,3]-dioxolane(DLin-K-DMA), 1,2-dilinoleylcarbamoyloxy-3-dimethylaminopropane(DLin-C-DAP), 1,2-dilinoleyoxy-3-(dimethylamino)acetoxypropane(DLin-DAC), 1,2-dilinoleyoxy-3-morpholinopropane (DLin-MA),1,2-dilinoleoyl-3-dimethylaminopropane (DLinDAP),1,2-dilinoleylthio-3-dimethylaminopropane (DLin-S-DMA),1-linoleoyl-2-linoleyloxy-3-dimethylaminopropane (DLin-2-DMAP),1,2-dilinoleyloxy-3-trimethylaminopropane chloride salt (DLin-TMA.Cl),1,2-dilinoleoyl-3-trimethylaminopropane chloride salt (DLin-TAP.Cl),1,2-dilinoleyloxy-3-(N-methylpiperazino)propane (DLin-MPZ),3-(N,N-dilinoleylamino)-1,2-propanediol (DLinAP),3-(N,N-dioleylamino)-1,2-propanedio (DOAP),1,2-dilinoleyloxo-3-(2-N,N-dimethylamino)ethoxypropane (DLin-EG-DMA), ormixtures thereof. In preferred embodiments, the cationic lipid ofFormula III is DLin-K-C2-DMA (XTC2).

The cationic lipid typically comprises from about 50 mol % to about 90mol %, from about 50 mol % to about 85 mol %, from about 50 mol % toabout 80 mol %, from about 50 mol % to about 75 mol %, from about 50 mol% to about 70 mol %, from about 50 mol % to about 65 mol %, or fromabout 55 mol % to about 65 mol % of the total lipid present in theparticle.

It will be readily apparent to one of skill in the art that depending onthe intended use of the particles, the proportions of the components canbe varied and the delivery efficiency of a particular formulation can bemeasured using, e.g., an endosomal release parameter (ERP) assay.

B. Non-Cationic Lipids

The non-cationic lipids used in the lipid particles of the invention(e.g., SNALP) can be any of a variety of neutral uncharged,zwitterionic, or anionic lipids capable of producing a stable complex.

Non-limiting examples of non-cationic lipids include phospholipids suchas lecithin, phosphatidylethanolamine, lysolecithin,lysophosphatidylethanolamine, phosphatidylserine, phosphatidylinositol,sphingomyelin, egg sphingomyelin (ESM), cephalin, cardiolipin,phosphatidic acid, cerebrosides, dicetylphosphate,distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine(DOPC), dipalmitoylphosphatidylcholine (DPPC),dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol(DPPG), dioleoylphosphatidylethanolamine (DOPE),palmitoyloleoyl-phosphatidylcholine (POPC),palmitoyloleoyl-phosphatidylethanolamine (POPE),palmitoyloleyol-phosphatidylglycerol (POPG),dioleoylphosphatidylethanolamine4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (DOPE-mal),dipalmitoyl-phosphatidylethanolamine (DPPE),dimyristoyl-phosphatidylethanolamine (DMPE),distearoyl-phosphatidylethanolamine (DSPE),monomethyl-phosphatidylethanolamine, dimethyl-phosphatidylethanolamine,dielaidoyl-phosphatidylethanolamine (DEPE),stearoyloleoyl-phosphatidylethanolamine (SOPE), lysophosphatidylcholine,dilinoleoylphosphatidylcholine, and mixtures thereof. Otherdiacylphosphatidylcholine and diacylphosphatidylethanolaminephospholipids can also be used. The acyl groups in these lipids arepreferably acyl groups derived from fatty acids having C₁₀-C₂₄ carbonchains, e.g., lauroyl, myristoyl, palmitoyl, stearoyl, or oleoyl.

Additional examples of non-cationic lipids include sterols such ascholesterol and derivatives thereof such as cholestanol, cholestanone,cholestenone, coprostanol, cholesteryl-2′-hydroxyethyl ether,cholesteryl-4′-hydroxybutyl ether, and mixtures thereof.

In some embodiments, the non-cationic lipid present in the lipidparticles (e.g., SNALP) comprises or consists of cholesterol or aderivative thereof, e.g., a phospholipid-free lipid particleformulation. In other embodiments, the non-cationic lipid present in thelipid particles (e.g., SNALP) comprises or consists of one or morephospholipids, e.g., a cholesterol-free lipid particle formulation. Infurther embodiments, the non-cationic lipid present in the lipidparticles (e.g., SNALP) comprises or consists of a mixture of one ormore phospholipids and cholesterol or a derivative thereof.

Other examples of non-cationic lipids suitable for use in the presentinvention include nonphosphorous containing lipids such as, e.g.,stearylamine, dodecylamine, hexadecylamine, acetyl palmitate,glycerolricinoleate, hexadecyl stereate, isopropyl myristate, amphotericacrylic polymers, triethanolamine-lauryl sulfate, alkyl-aryl sulfatepolyethyloxylated fatty acid amides, dioctadecyldimethyl ammoniumbromide, ceramide, sphingomyelin, and the like.

In some embodiments, the non-cationic lipid comprises from about 13 mol% to about 49.5 mol %, from about 20 mol % to about 45 mol %, from about25 mol % to about 45 mol %, from about 30 mol % to about 45 mol %, fromabout 35 mol % to about 45 mol %, from about 20 mol % to about 40 mol %,from about 25 mol % to about 40 mol %, or from about 30 mol % to about40 mol % of the total lipid present in the particle.

In certain embodiments, the cholesterol present in phospholipid-freelipid particles comprises from about 30 mol % to about 45 mol %, fromabout 30 mol % to about 40 mol %, from about 35 mol % to about 45 mol %,or from about 35 mol % to about 40 mol % of the total lipid present inthe particle. As a non-limiting example, a phospholipid-free lipidparticle may comprise cholesterol at about 37 mol % of the total lipidpresent in the particle.

In certain other embodiments, the cholesterol present in lipid particlescontaining a mixture of phospholipid and cholesterol comprises fromabout 30 mol % to about 40 mol %, from about 30 mol % to about 35 mol %,or from about 35 mol % to about 40 mol % of the total lipid present inthe particle. As a non-limiting example, a lipid particle comprising amixture of phospholipid and cholesterol may comprise cholesterol atabout 34 mol % of the total lipid present in the particle.

In further embodiments, the cholesterol present in lipid particlescontaining a mixture of phospholipid and cholesterol comprises fromabout 10 mol % to about 30 mol %, from about 15 mol % to about 25 mol %,or from about 17 mol % to about 23 mol % of the total lipid present inthe particle. As a non-limiting example, a lipid particle comprising amixture of phospholipid and cholesterol may comprise cholesterol atabout 20 mol % of the total lipid present in the particle.

In embodiments where the lipid particles contain a mixture ofphospholipid and cholesterol or a cholesterol derivative, the mixturemay comprise up to about 40, 45, 50, 55, or 60 mol % of the total lipidpresent in the particle. In certain instances, the phospholipidcomponent in the mixture may comprise from about 2 mol % to about 12 mol%, from about 4 mol % to about 10 mol %, from about 5 mol % to about 10mol %, from about 5 mol % to about 9 mol %, or from about 6 mol % toabout 8 mol % of the total lipid present in the particle. As anon-limiting example, a lipid particle comprising a mixture ofphospholipid and cholesterol may comprise a phospholipid such as DPPC orDSPC at about 7 mol % (e.g., in a mixture with about 34 mol %cholesterol) of the total lipid present in the particle. In certainother instances, the phospholipid component in the mixture may comprisefrom about 10 mol % to about 30 mol %, from about 15 mol % to about 25mol %, or from about 17 mol % to about 23 mol % of the total lipidpresent in the particle. As another non-limiting example, a lipidparticle comprising a mixture of phospholipid and cholesterol maycomprise a phospholipid such as DPPC or DSPC at about 20 mol % (e.g., ina mixture with about 20 mol % cholesterol) of the total lipid present inthe particle.

C. Lipid Conjugate

In addition to cationic and non-cationic lipids, the lipid particles ofthe invention (e.g., SNALP) comprise a lipid conjugate. The conjugatedlipid is useful in that it prevents the aggregation of particles.Suitable conjugated lipids include, but are not limited to, PEG-lipidconjugates, ATTA-lipid conjugates, cationic-polymer-lipid conjugates(CPLs), and mixtures thereof. In certain embodiments, the particlescomprise either a PEG-lipid conjugate or an ATTA-lipid conjugatetogether with a CPL.

In a preferred embodiment, the lipid conjugate is a PEG-lipid. Examplesof PEG-lipids include, but are not limited to, PEG coupled todialkyloxypropyls (PEG-DAA) as described in, e.g., PCT Publication No.WO 05/026372, PEG coupled to diacylglycerol (PEG-DAG) as described in,e.g., U.S. Patent Publication Nos. 20030077829 and 2005008689, PEGcoupled to phospholipids such as phosphatidylethanolamine (PEG-PE), PEGconjugated to ceramides as described in, e.g., U.S. Pat. No. 5,885,613,PEG conjugated to cholesterol or a derivative thereof, and mixturesthereof. The disclosures of these patent documents are hereinincorporated by reference in their entirety for all purposes. AdditionalPEG-lipids include, without limitation, PEG-C-DOMG, 2 KPEG-DMG, and amixture thereof.

PEG is a linear, water-soluble polymer of ethylene PEG repeating unitswith two terminal hydroxyl groups. PEGs are classified by theirmolecular weights; for example, PEG 2000 has an average molecular weightof about 2,000 daltons, and PEG 5000 has an average molecular weight ofabout 5,000 daltons. PEGs are commercially available from Sigma ChemicalCo. and other companies and include, for example, the following:monomethoxypolyethylene glycol (MePEG-OH), monomethoxypolyethyleneglycol-succinate (MePEG-S), monomethoxypolyethylene glycol-succinimidylsuccinate (MePEG-S-NHS), monomethoxypolyethylene glycol-amine(MePEG-NH₂), monomethoxypolyethylene glycol-tresylate (MePEG-TRES), andmonomethoxypolyethylene glycol-imidazolyl-carbonyl (MePEG-IM). OtherPEGs such as those described in U.S. Pat. Nos. 6,774,180 and 7,053,150(e.g., mPEG (20 KDa) amine) are also useful for preparing the PEG-lipidconjugates of the present invention. The disclosures of these patentsare herein incorporated by reference in their entirety for all purposes.In addition, monomethoxypolyethyleneglycolacetic acid (MePEG-CH₂COOH) isparticularly useful for preparing PEG-lipid conjugates including, e.g.,PEG-DAA conjugates.

The PEG moiety of the PEG-lipid conjugates described herein may comprisean average molecular weight ranging from about 550 daltons to about10,000 daltons. In certain instances, the PEG moiety has an averagemolecular weight of from about 750 daltons to about 5,000 daltons (e.g.,from about 1,000 daltons to about 5,000 daltons, from about 1,500daltons to about 3,000 daltons, from about 750 daltons to about 3,000daltons, from about 750 daltons to about 2,000 daltons, etc.). Inpreferred embodiments, the PEG moiety has an average molecular weight ofabout 2,000 daltons or about 750 daltons.

In certain instances, the PEG can be optionally substituted by an alkyl,alkoxy, acyl, or aryl group. The PEG can be conjugated directly to thelipid or may be linked to the lipid via a linker moiety. Any linkermoiety suitable for coupling the PEG to a lipid can be used including,e.g., non-ester containing linker moieties and ester-containing linkermoieties. In a preferred embodiment, the linker moiety is a non-estercontaining linker moiety. As used herein, the term “non-ester containinglinker moiety” refers to a linker moiety that does not contain acarboxylic ester bond (—OC(O)—). Suitable non-ester containing linkermoieties include, but are not limited to, amido (—C(O)NH—), amino(—NR—), carbonyl (—C(O)—), carbamate (—NHC(O)O—), urea (—NHC(O)NH—),disulphide (—S—S—), ether (—O—), succinyl (—(O)CCH₂CH₂C(O)—),succinamidyl (—NHC(O)CH₂CH₂C(O)NH—), ether, disulphide, as well ascombinations thereof (such as a linker containing both a carbamatelinker moiety and an amido linker moiety). In a preferred embodiment, acarbamate linker is used to couple the PEG to the lipid.

In other embodiments, an ester containing linker moiety is used tocouple the PEG to the lipid. Suitable ester containing linker moietiesinclude, e.g., carbonate (—OC(O)O—), succinoyl, phosphate esters(—O—(O)POH—O—), sulfonate esters, and combinations thereof.

Phosphatidylethanolamines having a variety of acyl chain groups ofvarying chain lengths and degrees of saturation can be conjugated to PEGto form the lipid conjugate. Such phosphatidylethanolamines arecommercially available, or can be isolated or synthesized usingconventional techniques known to those of skilled in the art.Phosphatidylethanolamines containing saturated or unsaturated fattyacids with carbon chain lengths in the range of C₁₀ to C₂₀ arepreferred. Phosphatidylethanolamines with mono- or diunsaturated fattyacids and mixtures of saturated and unsaturated fatty acids can also beused. Suitable phosphatidylethanolamines include, but are not limitedto, dimyristoyl-phosphatidylethanolamine (DMPE),dipalmitoyl-phosphatidylethanolamine (DPPE),dioleoylphosphatidylethanolamine (DOPE), anddistearoyl-phosphatidylethanolamine (DSPE).

The term “ATTR” or “polyamide” refers to, without limitation, compoundsdescribed in U.S. Pat. Nos. 6,320,017 and 6,586,559, the disclosures ofwhich are herein incorporated by reference in their entirety for allpurposes. These compounds include a compound having the formula:

wherein R is a member selected from the group consisting of hydrogen,alkyl and acyl; R¹ is a member selected from the group consisting ofhydrogen and alkyl; or optionally, R and R¹ and the nitrogen to whichthey are bound form an azido moiety; R² is a member of the groupselected from hydrogen, optionally substituted alkyl, optionallysubstituted aryl and a side chain of an amino acid; R³ is a memberselected from the group consisting of hydrogen, halogen, hydroxy,alkoxy, mercapto, hydrazino, amino and NR⁴R⁵, wherein R⁴ and R⁵ areindependently hydrogen or alkyl; n is 4 to 80; m is 2 to 6; p is 1 to 4;and q is 0 or 1. It will be apparent to those of skill in the art thatother polyamides can be used in the compounds of the present invention.

The term “diacylglycerol” refers to a compound having 2 fatty acylchains, R¹ and R², both of which have independently between 2 and 30carbons bonded to the 1- and 2-position of glycerol by ester linkages.The acyl groups can be saturated or have varying degrees ofunsaturation. Suitable acyl groups include, but are not limited to,lauryl (C₁₂), myristyl (C₁₄), palmityl (C₁₆), stearyl (C₁₈), and icosyl(C₂₀). In preferred embodiments, R¹ and R² are the same, i.e., R¹ and R²are both myristyl (i.e., dimyristyl), R¹ and R² are both stearyl (i.e.,distearyl), etc. Diacylglycerols have the following general formula:

The term “dialkyloxypropyl” refers to a compound having 2 alkyl chains,R¹ and R², both of which have independently between 2 and 30 carbons.The alkyl groups can be saturated or have varying degrees ofunsaturation. Dialkyloxypropyls have the following general formula:

In a preferred embodiment, the PEG-lipid is a PEG-DAA conjugate havingthe following formula:

wherein R¹ and R² are independently selected and are long-chain alkylgroups having from about 10 to about 22 carbon atoms; PEG is apolyethyleneglycol; and L is a non-ester containing linker moiety or anester containing linker moiety as described above. The long-chain alkylgroups can be saturated or unsaturated. Suitable alkyl groups include,but are not limited to, lauryl (C₁₂), myristyl (C₁₄), palmityl (C₁₆),stearyl (C₁₈), and icosyl (C₂₀). In preferred embodiments, R¹ and R² arethe same, i.e., R¹ and R² are both myristyl (i.e., dimyristyl), R¹ andR² are both stearyl (i.e., distearyl), etc.

In Formula VII above, the PEG has an average molecular weight rangingfrom about 550 daltons to about 10,000 daltons. In certain instances,the PEG has an average molecular weight of from about 750 daltons toabout 5,000 daltons (e.g., from about 1,000 daltons to about 5,000daltons, from about 1,500 daltons to about 3,000 daltons, from about 750daltons to about 3,000 daltons, from about 750 daltons to about 2,000daltons, etc.). In preferred embodiments, the PEG has an averagemolecular weight of about 2,000 daltons or about 750 daltons. The PEGcan be optionally substituted with alkyl, alkoxy, acyl, or aryl. Incertain embodiments, the terminal hydroxyl group is substituted with amethoxy or methyl group.

In a preferred embodiment, “L” is a non-ester containing linker moiety.Suitable non-ester containing linkers include, but are not limited to,an amido linker moiety, an amino linker moiety, a carbonyl linkermoiety, a carbamate linker moiety, a urea linker moiety, an ether linkermoiety, a disulphide linker moiety, a succinamidyl linker moiety, andcombinations thereof. In a preferred embodiment, the non-estercontaining linker moiety is a carbamate linker moiety (i.e., a PEG-C-DAAconjugate). In another preferred embodiment, the non-ester containinglinker moiety is an amido linker moiety (i.e., a PEG-A-DAA conjugate).In yet another preferred embodiment, the non-ester containing linkermoiety is a succinamidyl linker moiety (i.e., a PEG-S-DAA conjugate).

In particular embodiments, the PEG-lipid conjugate is selected from:

The PEG-DAA conjugates are synthesized using standard techniques andreagents known to those of skill in the art. It will be recognized thatthe PEG-DAA conjugates will contain various amide, amine, ether, thio,carbamate, and urea linkages. Those of skill in the art will recognizethat methods and reagents for forming these bonds are well known andreadily available. See, e.g., March, ADVANCED ORGANIC CHEMISTRY (Wiley1992); Larock, COMPREHENSIVE ORGANIC TRANSFORMATIONS (VCH 1989); andFurniss, VOGEL'S TEXTBOOK OF PRACTICAL ORGANIC CHEMISTRY, 5th ed.(Longman 1989). It will also be appreciated that any functional groupspresent may require protection and deprotection at different points inthe synthesis of the PEG-DAA conjugates. Those of skill in the art willrecognize that such techniques are well known. See, e.g., Green andWuts, PROTECTIVE GROUPS IN ORGANIC SYNTHESIS (Wiley 1991).

Preferably, the PEG-DAA conjugate is a dilauryloxypropyl (C₁₂)-PEGconjugate, dimyristyloxypropyl (C₁₄)-PEG conjugate, adipalmityloxypropyl (C₁₆)-PEG conjugate, or a distearyloxypropyl(C₁₈)-PEG conjugate. Those of skill in the art will readily appreciatethat other dialkyloxypropyls can be used in the PEG-DAA conjugates ofthe present invention.

In addition to the foregoing, it will be readily apparent to those ofskill in the art that other hydrophilic polymers can be used in place ofPEG. Examples of suitable polymers that can be used in place of PEGinclude, but are not limited to, polyvinylpyrrolidone,polymethyloxazoline, polyethyloxazoline, polyhydroxypropylmethacrylamide, polymethacrylamide and polydimethylacrylamide,polylactic acid, polyglycolic acid, and derivatized celluloses such ashydroxymethylcellulose or hydroxyethylcellulose.

In addition to the foregoing components, the particles (e.g., SNALP orSPLP) of the present invention can further comprise cationicpoly(ethylene glycol) (PEG) lipids or CPLs (see, e.g., Chen et al.,Bioconj. Chem., 11:433-437 (2000)). Suitable SPLPs and SPLP-CPLs for usein the present invention, and methods of making and using SPLPs andSPLP-CPLs, are disclosed, e.g., in U.S. Pat. No. 6,852,334 and PCTPublication No. WO 00/62813, the disclosures of which are hereinincorporated by reference in their entirety for all purposes.

Suitable CPLs include compounds of Formula VIII:A-W—Y  (VIII),wherein A, W, and Y are as described below.

With reference to Formula VIII, “A” is a lipid moiety such as anamphipathic lipid, a neutral lipid, or a hydrophobic lipid that acts asa lipid anchor. Suitable lipid examples include, but are not limited to,diacylglycerolyls, dialkylglycerolyls, N—N-dialkylaminos,1,2-diacyloxy-3-aminopropanes, and 1,2-dialkyl-3-aminopropanes.

“W” is a polymer or an oligomer such as a hydrophilic polymer oroligomer. Preferably, the hydrophilic polymer is a biocompatable polymerthat is nonimmunogenic or possesses low inherent immunogenicity.Alternatively, the hydrophilic polymer can be weakly antigenic if usedwith appropriate adjuvants. Suitable nonimmunogenic polymers include,but are not limited to, PEG, polyamides, polylactic acid, polyglycolicacid, polylactic acid/polyglycolic acid copolymers, and combinationsthereof. In a preferred embodiment, the polymer has a molecular weightof from about 250 to about 7,000 daltons.

“Y” is a polycationic moiety. The term polycationic moiety refers to acompound, derivative, or functional group having a positive charge,preferably at least 2 positive charges at a selected pH, preferablyphysiological pH. Suitable polycationic moieties include basic aminoacids and their derivatives such as arginine, asparagine, glutamine,lysine, and histidine; spermine; spermidine; cationic dendrimers;polyamines; polyamine sugars; and amino polysaccharides. Thepolycationic moieties can be linear, such as linear tetralysine,branched or dendrimeric in structure. Polycationic moieties have betweenabout 2 to about 15 positive charges, preferably between about 2 toabout 12 positive charges, and more preferably between about 2 to about8 positive charges at selected pH values. The selection of whichpolycationic moiety to employ may be determined by the type of particleapplication which is desired.

The charges on the polycationic moieties can be either distributedaround the entire particle moiety, or alternatively, they can be adiscrete concentration of charge density in one particular area of theparticle moiety e.g., a charge spike. If the charge density isdistributed on the particle, the charge density can be equallydistributed or unequally distributed. All variations of chargedistribution of the polycationic moiety are encompassed by the presentinvention.

The lipid “A” and the nonimmunogenic polymer “W” can be attached byvarious methods and preferably by covalent attachment. Methods known tothose of skill in the art can be used for the covalent attachment of “A”and “W.” Suitable linkages include, but are not limited to, amide,amine, carboxyl, carbonate, carbamate, ester, and hydrazone linkages. Itwill be apparent to those skilled in the art that “A” and “W” must havecomplementary functional groups to effectuate the linkage. The reactionof these two groups, one on the lipid and the other on the polymer, willprovide the desired linkage. For example, when the lipid is adiacylglycerol and the terminal hydroxyl is activated, for instance withNHS and DCC, to form an active ester, and is then reacted with a polymerwhich contains an amino group, such as with a polyamide (see, e.g., U.S.Pat. Nos. 6,320,017 and 6,586,559, the disclosures of which are hereinincorporated by reference in their entirety for all purposes), an amidebond will form between the two groups.

In certain instances, the polycationic moiety can have a ligandattached, such as a targeting ligand or a chelating moiety forcomplexing calcium. Preferably, after the ligand is attached, thecationic moiety maintains a positive charge. In certain instances, theligand that is attached has a positive charge. Suitable ligands include,but are not limited to, a compound or device with a reactive functionalgroup and include lipids, amphipathic lipids, carrier compounds,bioaffinity compounds, biomaterials, biopolymers, biomedical devices,analytically detectable compounds, therapeutically active compounds,enzymes, peptides, proteins, antibodies, immune stimulators,radiolabels, fluorogens, biotin, drugs, haptens, DNA, RNA,polysaccharides, liposomes, virosomes, micelles, immunoglobulins,functional groups, other targeting moieties, or toxins.

The lipid conjugate (e.g., PEG-lipid) typically comprises from about 0.1mol % to about 2 mol %, from about 0.5 mol % to about 2 mol %, fromabout 1 mol % to about 2 mol %, from about 0.6 mol % to about 1.9 mol %,from about 0.7 mol % to about 1.8 mol %, from about 0.8 mol % to about1.7 mol %, from about 0.9 mol % to about 1.6 mol %, from about 0.9 mol %to about 1.8 mol %, from about 1 mol % to about 1.8 mol %, from about 1mol % to about 1.7 mol %, from about 1.2 mol % to about 1.8 mol %, fromabout 1.2 mol % to about 1.7 mol %, from about 1.3 mol % to about 1.6mol %, or from about 1.4 mol % to about 1.5 mol % of the total lipidpresent in the particle.

One of ordinary skill in the art will appreciate that the concentrationof the lipid conjugate can be varied depending on the lipid conjugateemployed and the rate at which the nucleic acid-lipid particle is tobecome fusogenic.

By controlling the composition and concentration of the lipid conjugate,one can control the rate at which the lipid conjugate exchanges out ofthe nucleic acid-lipid particle and, in turn, the rate at which thenucleic acid-lipid particle becomes fusogenic. For instance, when aPEG-phosphatidylethanolamine conjugate or a PEG-ceramide conjugate isused as the lipid conjugate, the rate at which the nucleic acid-lipidparticle becomes fusogenic can be varied, for example, by varying theconcentration of the lipid conjugate, by varying the molecular weight ofthe PEG, or by varying the chain length and degree of saturation of theacyl chain groups on the phosphatidylethanolamine or the ceramide. Inaddition, other variables including, for example, pH, temperature, ionicstrength, etc. can be used to vary and/or control the rate at which thenucleic acid-lipid particle becomes fusogenic. Other methods which canbe used to control the rate at which the nucleic acid-lipid particlebecomes fusogenic will become apparent to those of skill in the art uponreading this disclosure.

VI. Preparation of Lipid Particles

The lipid particles of the present invention, e.g., SNALP, in which anactive agent or therapeutic agent such as an interfering RNA isencapsulated in a lipid bilayer and is protected from degradation, canbe formed by any method known in the art including, but not limited to,a continuous mixing method or a direct dilution process.

In preferred embodiments, the cationic lipids are lipids of Formula I,II, and III, or combinations thereof. In other preferred embodiments,the non-cationic lipids are egg sphingomyelin (ESM),distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine(DOPC), 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC),dipalmitoyl-phosphatidylcholine (DPPC),monomethyl-phosphatidylethanolamine, dimethyl-phosphatidylethanolamine,14:0 PE (1,2-dimyristoyl-phosphatidylethanolamine (DMPE)), 16:0 PE(1,2-dipalmitoyl-phosphatidylethanolamine (DPPE)), 18:0 PE(1,2-distearoyl-phosphatidylethanolamine (DSPE)), 18:1 PE(1,2-dioleoyl-phosphatidylethanolamine (DOPE)), 18:1 trans PE(1,2-dielaidoyl-phosphatidylethanolamine (DEPE)), 18:0-18:1 PE(1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE)), 16:0-18:1 PE(1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE)), polyethyleneglycol-based polymers (e.g., PEG 2000, PEG 5000, PEG-modifieddiacylglycerols, or PEG-modified dialkyloxypropyls), cholesterol, orcombinations thereof.

In certain embodiments, the present invention provides for SNALPproduced via a continuous mixing method, e.g., a process that includesproviding an aqueous solution comprising a nucleic acid such as aninterfering RNA in a first reservoir, providing an organic lipidsolution in a second reservoir, and mixing the aqueous solution with theorganic lipid solution such that the organic lipid solution mixes withthe aqueous solution so as to substantially instantaneously produce aliposome encapsulating the nucleic acid (e.g., interfering RNA). Thisprocess and the apparatus for carrying this process are described indetail in U.S. Patent Publication No. 20040142025, the disclosure ofwhich is herein incorporated by reference in its entirety for allpurposes.

The action of continuously introducing lipid and buffer solutions into amixing environment, such as in a mixing chamber, causes a continuousdilution of the lipid solution with the buffer solution, therebyproducing a liposome substantially instantaneously upon mixing. As usedherein, the phrase “continuously diluting a lipid solution with a buffersolution” (and variations) generally means that the lipid solution isdiluted sufficiently rapidly in a hydration process with sufficientforce to effectuate vesicle generation. By mixing the aqueous solutioncomprising a nucleic acid with the organic lipid solution, the organiclipid solution undergoes a continuous stepwise dilution in the presenceof the buffer solution (i.e., aqueous solution) to produce a nucleicacid-lipid particle.

The SNALP formed using the continuous mixing method typically have asize of from about 40 nm to about 150 nm, from about 50 nm to about 150nm, from about 60 nm to about 130 nm, from about 70 nm to about 110 nm,or from about 70 nm to about 90 nm. The particles thus formed do notaggregate and are optionally sized to achieve a uniform particle size.

In another embodiment, the present invention provides for SNALP producedvia a direct dilution process that includes forming a liposome solutionand immediately and directly introducing the liposome solution into acollection vessel containing a controlled amount of dilution buffer. Inpreferred aspects, the collection vessel includes one or more elementsconfigured to stir the contents of the collection vessel to facilitatedilution. In one aspect, the amount of dilution buffer present in thecollection vessel is substantially equal to the volume of liposomesolution introduced thereto. As a non-limiting example, a liposomesolution in 45% ethanol when introduced into the collection vesselcontaining an equal volume of dilution buffer will advantageously yieldsmaller particles.

In yet another embodiment, the present invention provides for SNALPproduced via a direct dilution process in which a third reservoircontaining dilution buffer is fluidly coupled to a second mixing region.In this embodiment, the liposome solution formed in a first mixingregion is immediately and directly mixed with dilution buffer in thesecond mixing region. In preferred aspects, the second mixing regionincludes a T-connector arranged so that the liposome solution and thedilution buffer flows meet as opposing 180° flows; however, connectorsproviding shallower angles can be used, e.g., from about 27° to about180°. A pump mechanism delivers a controllable flow of buffer to thesecond mixing region. In one aspect, the flow rate of dilution bufferprovided to the second mixing region is controlled to be substantiallyequal to the flow rate of liposome solution introduced thereto from thefirst mixing region. This embodiment advantageously allows for morecontrol of the flow of dilution buffer mixing with the liposome solutionin the second mixing region, and therefore also the concentration ofliposome solution in buffer throughout the second mixing process. Suchcontrol of the dilution buffer flow rate advantageously allows for smallparticle size formation at reduced concentrations.

These processes and the apparatuses for carrying out these directdilution processes are described in detail in U.S. Patent PublicationNo. 20070042031, the disclosure of which is herein incorporated byreference in its entirety for all purposes.

The SNALP formed using the direct dilution process typically have a sizeof from about 40 nm to about 150 nm, from about 50 nm to about 150 nm,from about 60 nm to about 130 nm, from about 70 nm to about 110 nm, orfrom about 70 nm to about 90 nm. The particles thus formed do notaggregate and are optionally sized to achieve a uniform particle size.

If needed, the lipid particles of the invention (e.g., SNALP) can besized by any of the methods available for sizing liposomes. The sizingmay be conducted in order to achieve a desired size range and relativelynarrow distribution of particle sizes.

Several techniques are available for sizing the particles to a desiredsize. One sizing method, used for liposomes and equally applicable tothe present particles, is described in U.S. Pat. No. 4,737,323, thedisclosure of which is herein incorporated by reference in its entiretyfor all purposes. Sonicating a particle suspension either by bath orprobe sonication produces a progressive size reduction down to particlesof less than about 50 nm in size. Homogenization is another method whichrelies on shearing energy to fragment larger particles into smallerones. In a typical homogenization procedure, particles are recirculatedthrough a standard emulsion homogenizer until selected particle sizes,typically between about 60 and about 80 nm, are observed. In bothmethods, the particle size distribution can be monitored by conventionallaser-beam particle size discrimination, or QELS.

Extrusion of the particles through a small-pore polycarbonate membraneor an asymmetric ceramic membrane is also an effective method forreducing particle sizes to a relatively well-defined size distribution.Typically, the suspension is cycled through the membrane one or moretimes until the desired particle size distribution is achieved. Theparticles may be extruded through successively smaller-pore membranes,to achieve a gradual reduction in size.

In some embodiments, the nucleic acids in the SNALP are precondensed asdescribed in, e.g., U.S. patent application Ser. No. 09/744,103, thedisclosure of which is herein incorporated by reference in its entiretyfor all purposes.

In other embodiments, the methods will further comprise adding non-lipidpolycations which are useful to effect the lipofection of cells usingthe present compositions. Examples of suitable non-lipid polycationsinclude, hexadimethrine bromide (sold under the brandname POLYBRENE®,from Aldrich Chemical Co., Milwaukee, Wis., USA) or other salts ofhexadimethrine. Other suitable polycations include, for example, saltsof poly-L-ornithine, poly-L-arginine, poly-L-lysine, poly-D-lysine,polyallylamine, and polyethyleneimine. Addition of these salts ispreferably after the particles have been formed.

In some embodiments, the nucleic acid to lipid ratios (mass/mass ratios)in a formed SNALP will range from about 0.01 to about 0.2, from about0.02 to about 0.1, from about 0.03 to about 0.1, or from about 0.01 toabout 0.08. The ratio of the starting materials also falls within thisrange. In other embodiments, the SNALP preparation uses about 400 μgnucleic acid per 10 mg total lipid or a nucleic acid to lipid mass ratioof about 0.01 to about 0.08 and, more preferably, about 0.04, whichcorresponds to 1.25 mg of total lipid per 50 μg of nucleic acid. Inother preferred embodiments, the particle has a nucleic acid:lipid massratio of about 0.08.

In other embodiments, the lipid to nucleic acid ratios (mass/massratios) in a formed SNALP will range from about 1 (1:1) to about 100(100:1), from about 5 (5:1) to about 100 (100:1), from about 1 (1:1) toabout 50 (50:1), from about 2 (2:1) to about 50 (50:1), from about 3(3:1) to about 50 (50:1), from about 4 (4:1) to about 50 (50:1), fromabout 5 (5:1) to about 50 (50:1), from about 1 (1:1) to about 25 (25:1),from about 2 (2:1) to about 25 (25:1), from about 3 (3:1) to about 25(25:1), from about 4 (4:1) to about 25 (25:1), from about 5 (5:1) toabout 25 (25:1), from about 5 (5:1) to about 20 (20:1), from about 5(5:1) to about 15 (15:1), from about 5 (5:1) to about 10 (10:1), about 5(5:1), 6 (6:1), 7 (7:1), 8 (8:1), 9 (9:1), (10:1), 11 (11:1), 12 (12:1),13 (13:1), 14 (14:1), or 15 (15:1). The ratio of the starting materialsalso falls within this range.

As previously discussed, the conjugated lipid may further include a CPL.A variety of general methods for making SNALP-CPLs (CPL-containingSNALP) are discussed herein. Two general techniques include“post-insertion” technique, that is, insertion of a CPL into, forexample, a pre-formed SNALP, and the “standard” technique, wherein theCPL is included in the lipid mixture during, for example, the SNALPformation steps. The post-insertion technique results in SNALP havingCPLs mainly in the external face of the SNALP bilayer membrane, whereasstandard techniques provide SNALP having CPLs on both internal andexternal faces. The method is especially useful for vesicles made fromphospholipids (which can contain cholesterol) and also for vesiclescontaining PEG-lipids (such as PEG-DAAs and PEG-DAGs). Methods of makingSNALP-CPL, are taught, for example, in U.S. Pat. Nos. 5,705,385;6,586,410; 5,981,501; 6,534,484; and 6,852,334; U.S. Patent PublicationNo. 20020072121; and PCT Publication No. WO 00/62813, the disclosures ofwhich are herein incorporated by reference in their entirety for allpurposes.

VII. Kits

The present invention also provides lipid particles (e.g., SNALP) in kitform. The kit may comprise a container which is compartmentalized forholding the various elements of the lipid particles (e.g., the activeagents or therapeutic agents such as nucleic acids and the individuallipid components of the particles). In some embodiments, the kit mayfurther comprise an endosomal membrane destabilizer (e.g., calciumions). The kit typically contains the lipid particle compositions of thepresent invention, preferably in dehydrated form, with instructions fortheir rehydration and administration.

As explained herein, the lipid particles of the invention (e.g., SNALP)can be tailored to preferentially target particular tissues, organs, ortumors of interest. In certain instances, preferential targeting oflipid particles such as SNALP may be carried out by controlling thecomposition of the particle itself. For instance, as set forth inExample 11, it has been found that the 1:57 PEG-cDSA SNALP formulationcan be used to preferentially target tumors outside of the liver,whereas the 1:57 PEG-cDMA SNALP formulation can be used topreferentially target the liver (including liver tumors).

In certain other instances, it may be desirable to have a targetingmoiety attached to the surface of the lipid particle to further enhancethe targeting of the particle. Methods of attaching targeting moieties(e.g., antibodies, proteins, etc.) to lipids (such as those used in thepresent particles) are known to those of skill in the art.

VII. Administration of Lipid Particles

Once formed, the lipid particles of the invention (e.g., SNALP) areuseful for the introduction of active agents or therapeutic agents(e.g., nucleic acids such as interfering RNA) into cells. Accordingly,the present invention also provides methods for introducing an activeagent or therapeutic agent such as a nucleic acid (e.g., interferingRNA) into a cell. The methods are carried out in vitro or in vivo byfirst forming the particles as described above and then contacting theparticles with the cells for a period of time sufficient for delivery ofthe active agent or therapeutic agent to the cells to occur.

The lipid particles of the invention (e.g., SNALP) can be adsorbed toalmost any cell type with which they are mixed or contacted. Onceadsorbed, the particles can either be endocytosed by a portion of thecells, exchange lipids with cell membranes, or fuse with the cells.Transfer or incorporation of the active agent or therapeutic agent(e.g., nucleic acid) portion of the particle can take place via any oneof these pathways. In particular, when fusion takes place, the particlemembrane is integrated into the cell membrane and the contents of theparticle combine with the intracellular fluid.

The lipid particles of the invention (e.g., SNALP) can be administeredeither alone or in a mixture with a pharmaceutically-acceptable carrier(e.g., physiological saline or phosphate buffer) selected in accordancewith the route of administration and standard pharmaceutical practice.Generally, normal buffered saline (e.g., 135-150 mM NaCl) will beemployed as the pharmaceutically-acceptable carrier. Other suitablecarriers include, e.g., water, buffered water, 0.4% saline, 0.3%glycine, and the like, including glycoproteins for enhanced stability,such as albumin, lipoprotein, globulin, etc. Additional suitablecarriers are described in, e.g., REMINGTON'S PHARMACEUTICAL SCIENCES,Mack Publishing Company, Philadelphia, Pa., 17th ed. (1985). As usedherein, “carrier” includes any and all solvents, dispersion media,vehicles, coatings, diluents, antibacterial and antifungal agents,isotonic and absorption delaying agents, buffers, carrier solutions,suspensions, colloids, and the like. The phrase“pharmaceutically-acceptable” refers to molecular entities andcompositions that do not produce an allergic or similar untowardreaction when administered to a human.

The pharmaceutically-acceptable carrier is generally added followingparticle formation. Thus, after the particle is formed, the particle canbe diluted into pharmaceutically-acceptable carriers such as normalbuffered saline.

The concentration of particles in the pharmaceutical formulations canvary widely, i.e., from less than about 0.05%, usually at or at leastabout 2 to 5%, to as much as about 10 to 90% by weight, and will beselected primarily by fluid volumes, viscosities, etc., in accordancewith the particular mode of administration selected. For example, theconcentration may be increased to lower the fluid load associated withtreatment. This may be particularly desirable in patients havingatherosclerosis-associated congestive heart failure or severehypertension. Alternatively, particles composed of irritating lipids maybe diluted to low concentrations to lessen inflammation at the site ofadministration.

The pharmaceutical compositions of the present invention may besterilized by conventional, well-known sterilization techniques. Aqueoussolutions can be packaged for use or filtered under aseptic conditionsand lyophilized, the lyophilized preparation being combined with asterile aqueous solution prior to administration. The compositions cancontain pharmaceutically-acceptable auxiliary substances as required toapproximate physiological conditions, such as pH adjusting and bufferingagents, tonicity adjusting agents and the like, for example, sodiumacetate, sodium lactate, sodium chloride, potassium chloride, andcalcium chloride. Additionally, the particle suspension may includelipid-protective agents which protect lipids against free-radical andlipid-peroxidative damages on storage. Lipophilic free-radicalquenchers, such as alphatocopherol and water-soluble iron-specificchelators, such as ferrioxamine, are suitable.

A. In Vivo Administration

Systemic delivery for in vivo therapy, e.g., delivery of a therapeuticnucleic acid to a distal target cell via body systems such as thecirculation, has been achieved using nucleic acid-lipid particles suchas those described in PCT Publication Nos. WO 05/007196, WO 05/121348,WO 05/120152, and WO 04/002453, the disclosures of which are hereinincorporated by reference in their entirety for all purposes. Thepresent invention also provides fully encapsulated lipid particles thatprotect the nucleic acid from nuclease degradation in serum, arenonimmunogenic, are small in size, and are suitable for repeat dosing.

For in vivo administration, administration can be in any manner known inthe art, e.g., by injection, oral administration, inhalation (e.g.,intransal or intratracheal), transdermal application, or rectaladministration. Administration can be accomplished via single or divideddoses. The pharmaceutical compositions can be administered parenterally,i.e., intraarticularly, intravenously, intraperitoneally,subcutaneously, or intramuscularly. In some embodiments, thepharmaceutical compositions are administered intravenously orintraperitoneally by a bolus injection (see, e.g., U.S. Pat. No.5,286,634). Intracellular nucleic acid delivery has also been discussedin Straubringer et al., Methods Enzymol., 101:512 (1983); Mannino etal., Biotechniques, 6:682 (1988); Nicolau et al., Crit. Rev. Ther. DrugCarrier Syst., 6:239 (1989); and Behr, Acc. Chem. Res., 26:274 (1993).Still other methods of administering lipid-based therapeutics aredescribed in, for example, U.S. Pat. Nos. 3,993,754; 4,145,410;4,235,871; 4,224,179; 4,522,803; and 4,588,578. The lipid particles canbe administered by direct injection at the site of disease or byinjection at a site distal from the site of disease (see, e.g., Culver,HUMAN GENE THERAPY, MaryAnn Liebert, Inc., Publishers, New York. pp.70-71 (1994)). The disclosures of the above-described references areherein incorporated by reference in their entirety for all purposes.

The compositions of the present invention, either alone or incombination with other suitable components, can be made into aerosolformulations (i.e., they can be “nebulized”) to be administered viainhalation (e.g., intranasally or intratracheally) (see, Brigham et al.,Am. J. Sci., 298:278 (1989)). Aerosol formulations can be placed intopressurized acceptable propellants, such as dichlorodifluoromethane,propane, nitrogen, and the like.

In certain embodiments, the pharmaceutical compositions may be deliveredby intranasal sprays, inhalation, and/or other aerosol deliveryvehicles. Methods for delivering nucleic acid compositions directly tothe lungs via nasal aerosol sprays have been described, e.g., in U.S.Pat. Nos. 5,756,353 and 5,804,212. Likewise, the delivery of drugs usingintranasal microparticle resins and lysophosphatidyl-glycerol compounds(U.S. Pat. No. 5,725,871) are also well-known in the pharmaceuticalarts. Similarly, transmucosal drug delivery in the form of apolytetrafluoroetheylene support matrix is described in U.S. Pat. No.5,780,045. The disclosures of the above-described patents are hereinincorporated by reference in their entirety for all purposes.

Formulations suitable for parenteral administration, such as, forexample, by intraarticular (in the joints), intravenous, intramuscular,intradermal, intraperitoneal, and subcutaneous routes, include aqueousand non-aqueous, isotonic sterile injection solutions, which can containantioxidants, buffers, bacteriostats, and solutes that render theformulation isotonic with the blood of the intended recipient, andaqueous and non-aqueous sterile suspensions that can include suspendingagents, solubilizers, thickening agents, stabilizers, and preservatives.In the practice of this invention, compositions are preferablyadministered, for example, by intravenous infusion, orally, topically,intraperitoneally, intravesically, or intrathecally.

Generally, when administered intravenously, the lipid particleformulations are formulated with a suitable pharmaceutical carrier. Manypharmaceutically acceptable carriers may be employed in the compositionsand methods of the present invention. Suitable formulations for use inthe present invention are found, for example, in REMINGTON'SPHARMACEUTICAL SCIENCES, Mack Publishing Company, Philadelphia, Pa.,17th ed. (1985). A variety of aqueous carriers may be used, for example,water, buffered water, 0.4% saline, 0.3% glycine, and the like, and mayinclude glycoproteins for enhanced stability, such as albumin,lipoprotein, globulin, etc. Generally, normal buffered saline (135-150mM NaCl) will be employed as the pharmaceutically acceptable carrier,but other suitable carriers will suffice. These compositions can besterilized by conventional liposomal sterilization techniques, such asfiltration. The compositions may contain pharmaceutically acceptableauxiliary substances as required to approximate physiologicalconditions, such as pH adjusting and buffering agents, tonicityadjusting agents, wetting agents and the like, for example, sodiumacetate, sodium lactate, sodium chloride, potassium chloride, calciumchloride, sorbitan monolaurate, triethanolamine oleate, etc. Thesecompositions can be sterilized using the techniques referred to aboveor, alternatively, they can be produced under sterile conditions. Theresulting aqueous solutions may be packaged for use or filtered underaseptic conditions and lyophilized, the lyophilized preparation beingcombined with a sterile aqueous solution prior to administration.

In certain applications, the lipid particles disclosed herein may bedelivered via oral administration to the individual. The particles maybe incorporated with excipients and used in the form of ingestibletablets, buccal tablets, troches, capsules, pills, lozenges, elixirs,mouthwash, suspensions, oral sprays, syrups, wafers, and the like (see,e.g., U.S. Pat. Nos. 5,641,515, 5,580,579, and 5,792,451, thedisclosures of which are herein incorporated by reference in theirentirety for all purposes). These oral dosage forms may also contain thefollowing: binders, gelatin; excipients, lubricants, and/or flavoringagents. When the unit dosage form is a capsule, it may contain, inaddition to the materials described above, a liquid carrier. Variousother materials may be present as coatings or to otherwise modify thephysical form of the dosage unit. Of course, any material used inpreparing any unit dosage form should be pharmaceutically pure andsubstantially non-toxic in the amounts employed.

Typically, these oral formulations may contain at least about 0.1% ofthe lipid particles or more, although the percentage of the particlesmay, of course, be varied and may conveniently be between about 1% or 2%and about 60% or 70% or more of the weight or volume of the totalformulation. Naturally, the amount of particles in each therapeuticallyuseful composition may be prepared is such a way that a suitable dosagewill be obtained in any given unit dose of the compound. Factors such assolubility, bioavailability, biological half-life, route ofadministration, product shelf life, as well as other pharmacologicalconsiderations will be contemplated by one skilled in the art ofpreparing such pharmaceutical formulations, and as such, a variety ofdosages and treatment regimens may be desirable.

Formulations suitable for oral administration can consist of: (a) liquidsolutions, such as an effective amount of a packaged therapeutic agentsuch as nucleic acid (e.g., interfering RNA) suspended in diluents suchas water, saline, or PEG 400; (b) capsules, sachets, or tablets, eachcontaining a predetermined amount of a therapeutic agent such as nucleicacid (e.g., interfering RNA), as liquids, solids, granules, or gelatin;(c) suspensions in an appropriate liquid; and (d) suitable emulsions.Tablet forms can include one or more of lactose, sucrose, mannitol,sorbitol, calcium phosphates, corn starch, potato starch,microcrystalline cellulose, gelatin, colloidal silicon dioxide, talc,magnesium stearate, stearic acid, and other excipients, colorants,fillers, binders, diluents, buffering agents, moistening agents,preservatives, flavoring agents, dyes, disintegrating agents, andpharmaceutically compatible carriers. Lozenge forms can comprise atherapeutic agent such as nucleic acid (e.g., interfering RNA) in aflavor, e.g., sucrose, as well as pastilles comprising the therapeuticagent in an inert base, such as gelatin and glycerin or sucrose andacacia emulsions, gels, and the like containing, in addition to thetherapeutic agent, carriers known in the art.

In another example of their use, lipid particles can be incorporatedinto a broad range of topical dosage forms. For instance, a suspensioncontaining nucleic acid-lipid particles such as SNALP can be formulatedand administered as gels, oils, emulsions, topical creams, pastes,ointments, lotions, foams, mousses, and the like.

When preparing pharmaceutical preparations of the lipid particles of theinvention, it is preferable to use quantities of the particles whichhave been purified to reduce or eliminate empty particles or particleswith therapeutic agents such as nucleic acid associated with theexternal surface.

The methods of the present invention may be practiced in a variety ofhosts. Preferred hosts include mammalian species, such as primates(e.g., humans and chimpanzees as well as other nonhuman primates),canines, felines, equines, bovines, ovines, caprines, rodents (e.g.,rats and mice), lagomorphs, and swine.

The amount of particles administered will depend upon the ratio oftherapeutic agent (e.g., nucleic acid) to lipid, the particulartherapeutic agent (e.g., nucleic acid) used, the disease or disorderbeing treated, the age, weight, and condition of the patient, and thejudgment of the clinician, but will generally be between about 0.01 andabout 50 mg per kilogram of body weight, preferably between about 0.1and about 5 mg/kg of body weight, or about 10⁸-10¹⁰ particles peradministration (e.g., injection).

B. In Vitro Administration

For in vitro applications, the delivery of therapeutic agents such asnucleic acids (e.g., interfering RNA) can be to any cell grown inculture, whether of plant or animal origin, vertebrate or invertebrate,and of any tissue or type. In preferred embodiments, the cells areanimal cells, more preferably mammalian cells, and most preferably humancells.

Contact between the cells and the lipid particles, when carried out invitro, takes place in a biologically compatible medium. Theconcentration of particles varies widely depending on the particularapplication, but is generally between about 1 μmol and about 10 mmol.Treatment of the cells with the lipid particles is generally carried outat physiological temperatures (about 37° C.) for periods of time of fromabout 1 to 48 hours, preferably of from about 2 to 4 hours.

In one group of preferred embodiments, a lipid particle suspension isadded to 60-80% confluent plated cells having a cell density of fromabout 10³ to about 10⁵ cells/ml, more preferably about 2×10⁴ cells/ml.The concentration of the suspension added to the cells is preferably offrom about 0.01 to 0.2 μg/ml, more preferably about 0.1 μg/ml.

Using an Endosomal Release Parameter (ERP) assay, the deliveryefficiency of the SNALP or other lipid particle of the invention can beoptimized. An ERP assay is described in detail in U.S. PatentPublication No. 20030077829, the disclosure of which is hereinincorporated by reference in its entirety for all purposes. Moreparticularly, the purpose of an ERP assay is to distinguish the effectof various cationic lipids and helper lipid components of SNALP based ontheir relative effect on binding/uptake or fusion with/destabilizationof the endosomal membrane. This assay allows one to determinequantitatively how each component of the SNALP or other lipid particleaffects delivery efficiency, thereby optimizing the SNALP or other lipidparticle. Usually, an ERP assay measures expression of a reporterprotein (e.g., luciferase, β-galactosidase, green fluorescent protein(GFP), etc.), and in some instances, a SNALP formulation optimized foran expression plasmid will also be appropriate for encapsulating aninterfering RNA. In other instances, an ERP assay can be adapted tomeasure downregulation of transcription or translation of a targetsequence in the presence or absence of an interfering RNA (e.g., siRNA).By comparing the ERPs for each of the various SNALP or other lipidparticles, one can readily determine the optimized system, e.g., theSNALP or other lipid particle that has the greatest uptake in the cell.

C. Cells for Delivery of Lipid Particles

The compositions and methods of the present invention are used to treata wide variety of cell types, in vivo and in vitro. Suitable cellsinclude, e.g., hematopoietic precursor (stem) cells, fibroblasts,keratinocytes, hepatocytes, endothelial cells, skeletal and smoothmuscle cells, osteoblasts, neurons, quiescent lymphocytes, terminallydifferentiated cells, slow or noncycling primary cells, parenchymalcells, lymphoid cells, epithelial cells, bone cells, and the like. Inpreferred embodiments, an active agent or therapeutic agent such as aninterfering RNA (e.g., siRNA) is delivered to cancer cells such as,e.g., lung cancer cells, colon cancer cells, rectal cancer cells, analcancer cells, bile duct cancer cells, small intestine cancer cells,stomach (gastric) cancer cells, esophageal cancer cells, gallbladdercancer cells, liver cancer cells, pancreatic cancer cells, appendixcancer cells, breast cancer cells, ovarian cancer cells, cervical cancercells, prostate cancer cells, renal cancer cells, cancer cells of thecentral nervous system, glioblastoma tumor cells, skin cancer cells,lymphoma cells, choriocarcinoma tumor cells, head and neck cancer cells,osteogenic sarcoma tumor cells, and blood cancer cells.

In vivo delivery of lipid particles such as SNALP encapsulating aninterfering RNA (e.g., siRNA) is suited for targeting cells of any celltype. The methods and compositions can be employed with cells of a widevariety of vertebrates, including mammals, such as, e.g, canines,felines, equines, bovines, ovines, caprines, rodents (e.g., mice, rats,and guinea pigs), lagomorphs, swine, and primates (e.g. monkeys,chimpanzees, and humans).

To the extent that tissue culture of cells may be required, it iswell-known in the art. For example, Freshney, Culture of Animal Cells, aManual of Basic Technique, 3rd Ed., Wiley-Liss, New York (1994), Kuchleret al., Biochemical Methods in Cell Culture and Virology, Dowden,Hutchinson and Ross, Inc. (1977), and the references cited thereinprovide a general guide to the culture of cells. Cultured cell systemsoften will be in the form of monolayers of cells, although cellsuspensions are also used.

D. Detection of Lipid Particles

In some embodiments, the lipid particles of the present invention (e.g.,SNALP) are detectable in the subject at about 1, 2, 3, 4, 5, 6, 7, 8 ormore hours. In other embodiments, the lipid particles of the presentinvention (e.g., SNALP) are detectable in the subject at about 8, 12,24, 48, 60, 72, or 96 hours, or about 6, 8, 10, 12, 14, 16, 18, 19, 22,24, 25, or 28 days after administration of the particles. The presenceof the particles can be detected in the cells, tissues, or otherbiological samples from the subject. The particles may be detected,e.g., by direct detection of the particles, detection of a therapeuticnucleic acid such as an interfering RNA (e.g., siRNA) sequence,detection of the target sequence of interest (i.e., by detectingexpression or reduced expression of the sequence of interest), or acombination thereof.

1. Detection of Particles

Lipid particles of the invention such as SNALP can be detected using anymethod known in the art. For example, a label can be coupled directly orindirectly to a component of the lipid particle using methods well-knownin the art. A wide variety of labels can be used, with the choice oflabel depending on sensitivity required, ease of conjugation with thelipid particle component, stability requirements, and availableinstrumentation and disposal provisions. Suitable labels include, butare not limited to, spectral labels such as fluorescent dyes (e.g.,fluorescein and derivatives, such as fluorescein isothiocyanate (FITC)and Oregon Green™; rhodamine and derivatives such Texas red,tetrarhodimine isothiocynate (TRITC), etc., digoxigenin, biotin,phycoerythrin, AMCA, CyDyes™, and the like; radiolabels such as ³H,¹²⁵I, ³⁵S, ¹⁴C, ³²P, ³³P, etc.; enzymes such as horse radish peroxidase,alkaline phosphatase, etc.; spectral colorimetric labels such ascolloidal gold or colored glass or plastic beads such as polystyrene,polypropylene, latex, etc. The label can be detected using any meansknown in the art.

2. Detection of Nucleic Acids

Nucleic acids (e.g., interfering RNA) are detected and quantified hereinby any of a number of means well-known to those of skill in the art. Thedetection of nucleic acids may proceed by well-known methods such asSouthern analysis, Northern analysis, gel electrophoresis, PCR,radiolabeling, scintillation counting, and affinity chromatography.Additional analytic biochemical methods such as spectrophotometry,radiography, electrophoresis, capillary electrophoresis, highperformance liquid chromatography (HPLC), thin layer chromatography(TLC), and hyperdiffusion chromatography may also be employed.

The selection of a nucleic acid hybridization format is not critical. Avariety of nucleic acid hybridization formats are known to those skilledin the art. For example, common formats include sandwich assays andcompetition or displacement assays. Hybridization techniques aregenerally described in, e.g., “Nucleic Acid Hybridization, A PracticalApproach,” Eds. Hames and Higgins, IRL Press (1985).

The sensitivity of the hybridization assays may be enhanced through useof a nucleic acid amplification system which multiplies the targetnucleic acid being detected. In vitro amplification techniques suitablefor amplifying sequences for use as molecular probes or for generatingnucleic acid fragments for subsequent subcloning are known. Examples oftechniques sufficient to direct persons of skill through such in vitroamplification methods, including the polymerase chain reaction (PCR) theligase chain reaction (LCR), Qβ-replicase amplification and other RNApolymerase mediated techniques (e.g., NASBA™) are found in Sambrook etal., In Molecular Cloning: A Laboratory Manual, Cold Spring HarborLaboratory Press (2000); and Ausubel et al., SHORT PROTOCOLS INMOLECULAR BIOLOGY, eds., Current Protocols, Greene PublishingAssociates, Inc. and John Wiley & Sons, Inc. (2002); as well as U.S.Pat. No. 4,683,202; PCR Protocols, A Guide to Methods and Applications(Innis et al. eds.) Academic Press Inc. San Diego, Calif. (1990);Arnheim & Levinson (Oct. 1, 1990), C&EN 36; The Journal Of NIH Research,3:81 (1991); Kwoh et al., Proc. Natl. Acad. Sci. USA, 86:1173 (1989);Guatelli et al., Proc. Natl. Acad. Sci. USA, 87:1874 (1990); Lomell etal., J. Clin. Chem., 35:1826 (1989); Landegren et al., Science, 241:1077(1988); Van Brunt, Biotechnology, 8:291 (1990); Wu and Wallace, Gene,4:560 (1989); Barringer et al., Gene, 89:117 (1990); and Sooknanan andMalek, Biotechnology, 13:563 (1995). Improved methods of cloning invitro amplified nucleic acids are described in U.S. Pat. No. 5,426,039.Other methods described in the art are the nucleic acid sequence basedamplification (NASBA™, Cangene, Mississauga, Ontario) and Qβ-replicasesystems. These systems can be used to directly identify mutants wherethe PCR or LCR primers are designed to be extended or ligated only whena select sequence is present. Alternatively, the select sequences can begenerally amplified using, for example, nonspecific PCR primers and theamplified target region later probed for a specific sequence indicativeof a mutation. The disclosures of the above-described references areherein incorporated by reference in their entirety for all purposes.

Nucleic acids for use as probes, e.g., in in vitro amplificationmethods, for use as gene probes, or as inhibitor components aretypically synthesized chemically according to the solid phasephosphoramidite triester method described by Beaucage et al.,Tetrahedron Letts., 22:1859 1862 (1981), e.g., using an automatedsynthesizer, as described in Needham VanDevanter et al., Nucleic AcidsRes., 12:6159 (1984). Purification of polynucleotides, where necessary,is typically performed by either native acrylamide gel electrophoresisor by anion exchange HPLC as described in Pearson et al., J. Chrom.,255:137 149 (1983). The sequence of the synthetic polynucleotides can beverified using the chemical degradation method of Maxam and Gilbert(1980) in Grossman and Moldave (eds.) Academic Press, New York, Methodsin Enzymology, 65:499.

An alternative means for determining the level of transcription is insitu hybridization. In situ hybridization assays are well-known and aregenerally described in Angerer et al., Methods Enzymol., 152:649 (1987).In an in situ hybridization assay, cells are fixed to a solid support,typically a glass slide. If DNA is to be probed, the cells are denaturedwith heat or alkali. The cells are then contacted with a hybridizationsolution at a moderate temperature to permit annealing of specificprobes that are labeled. The probes are preferably labeled withradioisotopes or fluorescent reporters.

VIII. Examples

The present invention will be described in greater detail by way ofspecific examples. The following examples are offered for illustrativepurposes, and are not intended to limit the invention in any manner.Those of skill in the art will readily recognize a variety ofnoncritical parameters which can be changed or modified to yieldessentially the same results.

Example 1 Materials and Methods

siRNA: All siRNA molecules used in these studies were chemicallysynthesized by the University of Calgary (Calgary, AB) or Dharmacon Inc.(Lafayette, Colo.). The siRNAs were desalted and annealed using standardprocedures.

Lipid Encapsulation of siRNA: In some embodiments, siRNA molecules wereencapsulated into nucleic acid-lipid particles composed of the followinglipids: the lipid conjugate PEG-cDMA (3-N—[(-Methoxypoly(ethyleneglycol)2000)carbamoyl]-1,2-dimyristyloxypropylamine); the cationic lipidDLinDMA (1,2-Dilinoleyloxy-3-(N,N-dimethyl)aminopropane); thephospholipid DPPC (1,2-Dipalmitoyl-sn-glycero-3-phosphocholine; AvantiPolar Lipids; Alabaster, Ala.); and synthetic cholesterol (Sigma-AldrichCorp.; St. Louis, Mo.) in the molar ratio 1.4:57.1:7.1:34.3,respectively. In other words, siRNAs were encapsulated into SNALP of thefollowing “1:57” formulation: 1.4% PEG-cDMA; 57.1% DLinDMA; 7.1% DPPC;and 34.3% cholesterol. In other embodiments, siRNA molecules wereencapsulated into phospholipid-free SNALP composed of the followinglipids: the lipid conjugate PEG-cDMA; the cationic lipid DLinDMA; andsynthetic cholesterol in the molar ratio 1.5:61.5:36.9, respectively. Inother words, siRNAs were encapsulated into phospholipid-free SNALP ofthe following “1:62” formulation: 1.5% PEG-cDMA; 61.5% DLinDMA; and36.9% cholesterol. For vehicle controls, empty particles with identicallipid composition were formed in the absence of siRNA. It should beunderstood that the 1:57 formulation and 1:62 formulation are targetformulations, and that the amount of lipid (both cationic andnon-cationic) present and the amount of lipid conjugate present in theformulation may vary. Typically, in the 1:57 formulation, the amount ofcationic lipid will be 57 mol %±5 mol %, and the amount of lipidconjugate will be 1.5 mol %±0.5 mol %, with the balance of the 1:57formulation being made up of non-cationic lipid (e.g., phospholipid,cholesterol, or a mixture of the two). Similarly, in the 1:62formulation, the amount of cationic lipid will be 62 mol %±5 mol %, andthe amount of lipid conjugate will be 1.5 mol %±0.5 mol %, with thebalance of the 1:62 formulation being made up of the non-cationic lipid(e.g., cholesterol).

Example 2 Eg5 siRNA Formulated as 1:57 SNALP Are Potent Inhibitors ofCell Growth In Vitro

SNALP formulations were prepared with an siRNA targeting Eg5 as thenucleic acid component. Eg5 is a member of kinesin-related proteins thatare involved in functions related to movements of organelles,microtubules, or chromosomes along microtubules. These functions includeaxonal transport, microtubule sliding during nuclear fusion or division,and chromosome disjunction during meiosis and early mitosis. Eg5 plays acritical role in mitosis of mammalian cells. The Eg5 siRNA used in thisstudy is provided in Table 1. The modifications involved introducing2′OMe-uridine at selected positions in the sense and antisense strandsof the Eg5 2263 siRNA sequence, in which the siRNA duplex contained lessthan about 20% 2′OMe-modified nucleotides.

TABLE 1 siRNA duplex comprising sense andantisense Eg5 RNA polynucleotides. SEQ ID % 2′OMe- % Modified inModification Eg5 2263 siRNA sequence NO: Modified DS Region U/U     5′-CU GAAGACC U GAAGACAA U dTdT-3′ 1 6/42 = 14.3%  6/38 = 15.8% 3′-dTdTGAC UUC U GGAC U UCUGUUA-5′ 2 Column 1: “U/U” = 2′OMe-uridine modified siRNAduplex; Column 2: 2′OMe-modified nucleotides are indicated in bold andunderlined. The siRNA duplex can alternatively or additionally comprise2′-deoxy-2′-fluoro (2′F) nucleotides, 2′-deoxy nucleotides,2′-O-(2-methoxyethyl) (MOE) nucleotides, and/or locked nucleic acid(LNA) nucleotides. “dT” =deoxythymidine. Column 3: The number andpercentage of 2 ′OMe- modified nucleotides in the siRNA duplex areprovided. Column 4: The number and percentage of modified nucleotides inthe double-stranded (DS) region of the siRNA duplex are provided.

The lipid components and physical characteristics of the SNALPformulations are summarized in Table 2. The lipid:drug ratio isdescribed in units of mg total lipid per mg nucleic acid. Mean particlesize and polydispersity were measured on a Malvern InstrumentsZetasizer. Encapsulation of nucleic acid was measured using a Ribogreenassay essentially as described in Heyes et al., Journal of ControlledRelease, 107:276-287 (2005).

TABLE 2 Characteristics of the SNALP formulations used in this study.Formulation Composition, Mole % Sample PEG(2000)-C-DMA | DLinDMA |Lipid/Drug Finished Product Characterization No. DPPC | CholesterolRatio Size (nm) Polydispersity % Encapsulation 1 2 | 40 | 10 | 48 12.457 0.07 90 2 1.8 | 36.4 | 18.2 | 43.6 14.0 72 0.12 89 3 1.4 | 27.0 | 6.8| 64.9 16.5 70 0.12 92 4 1.3 | 25.3 | 12.7 | 60.8 18.1 76 0.07 93 5 3.9| 39.2 | 9.8 | 47.1 13.5 53 0.27 86 6 3.6 | 35.7 | 17.9 | 42.9 15.1 580.18 87 7 2.7 | 26.7 | 6.7 | 64.0 17.6 56 0.17 92 8 2.5 | 25.0 | 12.5 |60.0 19.2 61 0.13 92 9 1.4 | 57.1 | 7.1 | 34.3 17.8 84 0.10 88 10 1.3 |53.3 | 13.3 | 32.0 19.5 83 0.10 89 11 1.1 | 42.6 | 5.3 | 51.1 22.0 800.10 93 12 1.0 | 40.4 | 10.1 | 48.5 23.6 78 0.11 88 13 2.8 | 56.3 | 7.0| 33.8 19.0 62 0.14 80 14 2.6 | 52.6 | 13.2 | 31.6 20.6 66 0.14 82 152.1 | 42.1 | 5.3 | 50.5 23.1 71 0.16 91 16 2 | 40 | 10 | 48 24.7 67 0.1492

Silencing of Eg5 by siRNA transfection causes mitotic arrest andapoptosis in mammalian cells. Cell viability following transfection withSNALP containing an siRNA targeting Eg5 therefore provides a simplebiological readout of in vitro transfection efficiency. Cell viabilityof in vitro cell cultures was assessed using the commercial reagentCellTiter-Blue® (Promega Corp.; Madison, Wis.), a resazurin dye that isreduced by metabolically active cells to the fluorogenic productresorufin. The human colon cancer cell line HT29 was cultured usingstandard tissue culture techniques. 72 hours after SNALP application,CellTiter-Blue® reagent was added to the culture to quantify themetabolic activity of the cells, which is a measure of cell viability.Data are presented as a percent of cell viability relative to(“untreated”) control cells that received phosphate buffered saline(PBS) vehicle only.

FIG. 1 shows that the 1:57 SNALP formulation containing Eg5 2263 U/UsiRNA was among the most potent inhibitors of tumor cell growth at allsiRNA concentrations tested (see, FIG. 1B, Sample 9).

Example 3 ApoB siRNA Formulated as 1:57 SNALP have Potent SilencingActivity In Vivo

SNALP formulations were prepared with an siRNA targeting apolipoproteinB (ApoB) as the nucleic acid component. ApoB is the main apolipoproteinof chylomicrons and low density lipoproteins (LDL). Mutations in ApoBare associated with hypercholesterolemia. ApoB occurs in the plasma in 2main forms, ApoB48 and ApoB100, which are synthesized in the intestineand liver, respectively, due to an organ-specific stop codon. The ApoBsiRNA used in this study is provided in Table 3. The modificationsinvolved introducing 2′OMe-uridine or 2′OMe-guanosine at selectedpositions in the sense and antisense strands of the ApoB siRNA sequence,in which the siRNA duplex contained less than about 20% 2′OMe-modifiednucleotides.

TABLE 3siRNA duplex comprising sense and antisense ApoB RNA polynucleotides.SEQ ID % 2′OMe- % Modified in Position Modification ApoB siRNA sequenceNO: Modified DS Region 10048 U2/2 G1/2    5′-AGU G UCA U CACAC UGAAUACC-3′ 3 7/42 = 16.7% 7/38 = 18.4% 3′-GU U CACAGUAGU G U G AC UUAU-5′ 4 Column 1: The number refers to the nucleotide position of the5′base of the sense strand relative to the mouse ApoB mRNA sequenceXM_137955. Column 2: The numbers refer to the distribution of 2′OMechemical modifications in each strand. Column 3: 2′OMe-modifiednucleotides are indicated in bold and underlined. The siRNA duplex canalternatively or additionally comprise 2′-deoxy-2′-fluoro (2′F)nucleotides, 2′-deoxy-nucleotides, 2 ′-O-(2-methoxyethyl) (MOE)nucleotides, and/or locked nucleic acid (LNA) nucleotides. Column 4: Thenumber and percentage of 2 ′OMe-modified nucleotides in the siRNA duplexare provided. Column 5: The number and percentage of modifiednucleotides in the double-stranded (DS) region of the siRNA duplex areprovided.

The lipid components and physical characteristics of the formulationsare summarized in Table 4. The lipid:drug ratio is described in units ofmg total lipid per mg nucleic acid. Mean particle size andpolydispersity were measured on a Malvern Instruments Zetasizer.Encapsulation of nucleic acid was measured using a Ribogreen assayessentially as described in Heyes et al., Journal of Controlled Release,107:276-287 (2005).

TABLE 4 Characteristics of the SNALP formulations used in this study.Formulation Composition Lipid/Drug Finished Product CharacterizationGroup Lipid Name & Mole % Ratio Size (nm) Polydispersity % Encapsulation2 PEG(2000)-C-DMA | DLinDMA | DPPC | Cholesterol 12.4 59 0.15 93 2 | 40| 10 | 48 3 PEG(2000)-C-DMA | DLinDMA | Cholesterol 10.7 55 0.17 91 2.2| 44.4 | 53.3 4 PEG(2000)-C-DMA | DLinDMA | DOPC | Cholesterol 12.5 590.16 92 2 | 40 | 10 | 48 5 PEG(2000)-C-DMA | DLinDMA | DMPC |Cholesterol 12.2 56 0.11 92 2 | 40 | 10 | 48 6 PEG(2000)-C-DMA | DLinDMA| DPPE | Cholesterol 13.8 66 0.16 93 1.8 | 36.4 | 18.2 | 43.6 7PEG(2000)-C-DMA | DLinDMA | DPPC | Cholestanol 12.4 56 0.12 92 2 | 40 |10 | 48 8 PEG(2000)-C-DMA | DLinDMA | DPPC | Cholesterol 16.5 60 0.10 931.4 | 27.0 | 6.8 | 64.9 9 PEG(2000)-C-DMA | DLinDMA | DPPC | Cholesterol18.1 74 0.13 92 1.3 | 25.3 | 12.7 | 60.8 10 PEG(2000)-C-DMA | DLinDMA |DPPC | Cholesterol 19.2 60 0.13 93 2.5 | 25.0 | 12.5 | 60.0 11PEG(2000)-C-DMA | DLinDMA | DPPC | Cholesterol 17.8 79 0.09 94 1.4 |57.1 | 7.4 | 34.3 12 PEG(2000)-C-DMA | DLinDMA | DPPC | Cholesterol 23.672 0.11 93 1.0 | 40.4 | 10.1 | 48.5 13 PEG(2000)-C-DMA | DLinDMA | DPPC8.7 73 0.09 87 2 | 70 | 28 14 PEG(2000)-C-DMA | DLinDMA | DPPC 11.3 650.11 87 1.6 | 54.7 | 43.8

BALB/c mice (female, at least 4 weeks old) were obtained from HarlanLabs. After an acclimation period (of at least 7 days), animals wereadministered SNALP by intravenous (IV) injection in the lateral tailvein once daily on Study Day 0 (1 dose total per animal). Dosage was 1mg encapsulated siRNA per kg body weight, corresponding to 10 ml/kg(rounded to the nearest 10 μl). As a negative control, one group ofanimals was given an IV injection of phosphate buffered saline (PBS)vehicle. On Study Day 2, animals were euthanized and liver tissue wascollected in RNAlater.

Liver tissues were analyzed for ApoB mRNA levels normalized againstglyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA levels using theQuantiGene assay (Panomics; Fremont, Calif.) essentially as described inJudge et al., Molecular Therapy, 13:494 (2006).

FIG. 2 shows that the 1:57 SNALP formulation containing ApoB 10048 U2/2G1/2 siRNA was the most potent at reducing ApoB expression in vivo (see,Group 11).

Example 4 ApoB siRNA Formulated as 1:57 SNALP have Potent SilencingActivity In Vivo

SNALP formulations were prepared with the ApoB siRNA set forth in Table3. The lipid components and physical characteristics of the formulationsare summarized in Table 5.

The lipid:drug ratio is described in units of mg total lipid per mgnucleic acid. Mean particle size and polydispersity were measured on aMalvern Instruments Zetasizer. Encapsulation of nucleic acid wasmeasured using a Ribogreen assay essentially as described in Heyes etal., Journal of Controlled Release, 107:276-287 (2005).

TABLE 5 Characteristics of the SNALP formulations used in this study.SNALP Particle Size % (L:D ratio) siRNA Payload (Polydispersity)Encapsulation 2:30 (13) ApoB-10048 U2/2 G1/2 65 nm (0.16) 88 1:57 (9)ApoB-10048 U2/2 G1/2 74 nm (0.10) 89

The 2:30 SNALP formulation used in this study is lipid composition2:30:20:48 as described in molar percentages of PEG-C-DMA, DLinDMA,DSPC, and cholesterol (in that order). This formulation was prepared bysyringe press at an input lipid to drug (L:D) ratio (mg:mg) of 13:1.

The 1:57 SNALP formulation used in this study is lipid composition1.5:57.1:7:34.3 as described in molar percentages of PEG-C-DMA, DLinDMA,DPPC, and cholesterol (in that order). This formulation was prepared bysyringe press at an input lipid to drug (L:D) ratio (mg:mg) of 9:1.

BALB/c mice (female, 4 weeks old) were obtained from Harlan Labs. Afteran acclimation period (of at least 7 days), animals were administeredSNALP by intravenous (IV) injection in the lateral tail vein once dailyon Study Days 0, 1, 2, 3 & 4 for a total of 5 doses per animal. Dailydosage was either 1.0 (for 2:30 SNALP) or 0.1 (for 1:57 SNALP) mgencapsulated siRNA per kg body weight, corresponding to 10 ml/kg(rounded to the nearest 10 μl). As a negative control, one group ofanimals was given IV injections of phosphate buffered saline (PBS)vehicle. On Study Day 7, 72 h after the last treatment, animals wereeuthanized and liver tissue was collected in RNAlater.

Liver tissues were analyzed for ApoB mRNA levels normalized againstglyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA levels using theQuantiGene assay (Panomics; Fremont, Calif.) essentially as described inJudge et al., Molecular Therapy, 13:494 (2006).

FIG. 3 shows that the 1:57 SNALP containing ApoB 10048 U2/2 G1/2 siRNAwas more than 10 times as efficacious as the 2:30 SNALP in mediatingApoB gene silencing in mouse liver at a 10-fold lower dose.

Example 5 ApoB siRNA Formulated as 1:57 or 1:62 SNALP have PotentSilencing Activity In Vivo

SNALP formulations were prepared with the ApoB siRNA set forth in Table3. The lipid components and physical characteristics of the formulationsare summarized in Table 6. The lipid:drug ratio is described in units ofmg total lipid per mg nucleic acid. Mean particle size andpolydispersity were measured on a Malvern Instruments Zetasizer.Encapsulation of nucleic acid was measured using a Ribogreen assayessentially as described in Heyes et al., Journal of Controlled Release,107:276-287 (2005).

TABLE 6 Characteristics of the SNALP formulations used in this study.Formulation Composition Lipid/Drug Finished Product CharacterizationGroup Lipid Name & Mole % Ratio Size (nm) Polydispersity % Encapsulation2 PEG(2000)-C-DMA | DLinDMA | DPPC | Cholesterol 8.9 76 0.06 89 1.4 |57.1 | 7.1 | 34.3 3 PEG(2000)-C-DMA | DLinDMA | Cholesterol 8.1 76 0.0486 1.5 | 61.5 | 36.9 4 PEG(2000)-C-DMA | DODMA | DPPC | Cholesterol 9.072 0.05 95 1.4 | 57.1 | 7.1 | 34.3 5 PEG(5000)-C-DMA | DLinDMA | DPPC |Cholesterol 9.6 52 0.16 89 1.4 | 57.1 | 7.1 | 34.3 6 PEG(2000)-C-DMA |DLinDMA | DPPC | Cholestanol 8.9 68 0.10 94 1.4 | 57.1 | 7.1 | 34.3 7PEG(2000)-C-DMA | DLinDMA | DPPE | Cholesterol 8.9 72 0.07 95 1.4 | 57.1| 7.1 | 34.3 8 PEG(2000)-C-DMA | DLinDMA | DPPC 8.6 74 0.13 86 1.8 |70.2 | 28.1

BALB/c mice (female, at least 4 weeks old) were obtained from HarlanLabs. After an acclimation period (of at least 7 days), animals wereadministered SNALP by intravenous (IV) injection in the lateral tailvein once daily on Study Day 0 (1 dose total per animal). Dosage was0.75 mg encapsulated siRNA per kg body weight, corresponding to 10 ml/kg(rounded to the nearest 10 μl). As a negative control, one group ofanimals was given an IV injection of phosphate buffered saline (PBS)vehicle. On Study Day 2, animals were euthanized and liver tissue wascollected in RNAlater.

Liver tissues were analyzed for ApoB mRNA levels normalized againstglyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA levels using theQuantiGene assay (Panomics; Fremont, Calif.) essentially as described inJudge et al., Molecular Therapy, 13:494 (2006).

FIG. 4 shows that the 1:57 and 1:62 SNALP formulations had comparableApoB silencing activity in vivo (see, e.g., Groups 2 & 3).

Example 6 ApoB siRNA Formulated as 1:62 SNALP have Potent SilencingActivity In Vivo

SNALP formulations were prepared with the ApoB siRNA set forth in Table3. The lipid components and physical characteristics of the formulationsare summarized in Table 7. The lipid:drug ratio is described in units ofmg total lipid per mg nucleic acid. Mean particle size andpolydispersity were measured on a Malvern Instruments Zetasizer.Encapsulation of nucleic acid was measured using a Ribogreen assayessentially as described in Heyes et al., Journal of Controlled Release,107:276-287 (2005).

TABLE 7 Characteristics of the SNALP formulations used in this study.Formulation Composition, Mole % PEG(2000)-C-DMA | DLinDMA | Lipid/DrugFinished Product Characterization Group Cholesterol Ratio Size (nm)Polydispersity % Encapsulation 2 1.5 | 61.5 | 36.9 6.1 80 0.07 92 3 1.4| 54.8 | 43.8 6.6 74 0.05 89 4 2.0 | 61.2 | 36.7 6.2 71 0.11 91 5 1.8 |54.5 | 43.6 6.7 67 0.09 91 6 1.3 | 68.1 | 30.6 7.4 91 0.06 89 7 1.2 |61.8 | 37.1 8.0 87 0.10 90 8 1.7 | 67.8 | 30.5 7.6 81 0.07 91 9 1.4 |56.3 | 42.3 8.6 75 0.11 92 10 1.9 | 61.3 | 36.8 8.2 72 0.10 91 11 1.8 |56.1 | 42.1 8.8 70 0.10 90 12 1.3 | 66.7 | 32.0 9.5 89 0.09 89 13 1.2 |61.7 | 37.0 10.0 87 0.10 91 14 1.7 | 66.4 | 31.9 9.6 82 0.11 90 15 1.5 |61.5 | 36.9 10.1 79 0.10 91

BALB/c mice (female, at least 4 weeks old) were obtained from HarlanLabs. After an acclimation period (of at least 7 days), animals wereadministered SNALP by intravenous (IV) injection in the lateral tailvein once daily on Study Day 0 (1 dose total per animal). Dosage was 0.1mg encapsulated siRNA per kg body weight, corresponding to 10 ml/kg(rounded to the nearest 10 μl). As a negative control, one group ofanimals was given an IV injection of phosphate buffered saline (PBS)vehicle. On Study Day 2, animals were euthanized and liver tissue wascollected in RNAlater.

Liver tissues were analyzed for ApoB mRNA levels normalized againstglyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA levels using theQuantiGene assay (Panomics; Fremont, Calif.) essentially as described inJudge et al., Molecular Therapy, 13:494 (2006).

FIG. 5 shows that the 1:62 SNALP formulation was one of the most potentinhibitors of ApoB expression at two different lipid:drug ratios (i.e.,6.1 & 10.1) among the phospholipid-free SNALP formulations tested (see,Groups 2 & 15).

Example 7 In Vivo Silencing of ApoB Expression Using 1:57 SNALP PreparedVia a Syringe Press or Gear Pump Process

This study illustrates a comparison of the tolerability and efficacy ofthe 1:57 SNALP formulation with ApoB-targeting siRNA as prepared byvarious manufacturing processes. In particular, 1:57 SNALP was preparedby a syringe press or gear pump process using either PBS or citratebuffer (post-blend dilution) and administered intravenously in mice.

Experimental Design

Animal Model: Female BALB/c mice, 5 wks old, n=4 per group/cage.

siRNA payload: ApoB10048 U2/2 G1/2 siRNA.

Tolerability:

IV Injection siRNA Lipid Group Formulation mg/kg mg/kg 1 PBS vehicleStandard 10 mL/kg volume 2 1|57 Citrate Direct Dil, Syringe 7 77 Press 31|57 PBS Direct Dil, Syringe Press 7 96 4 1|57 PBS Direct Dil, Gear Pump7 79 5 1|57 Citrate Direct Dil, Syringe 9 99 Press 6 1|57 PBS DirectDil, Syringe Press 9 123 7 1|57 PBS Direct Dil, Gear Pump 9 102Efficacy:

IV Injection siRNA Lipid Group Formulation mg/kg mg/kg 8 PBS vehicleStandard 10 mL/kg volume 9 1|57 PBS Direct Dil, Syringe Press 0.05 0.6810 1|57 PBS Direct Dil, Gear Pump 0.05 0.57 11 1|57 PBS Direct Dil,Syringe Press 0.1 1.36 12 1|57 PBS Direct Dil, Gear Pump 0.1 1.13Formulation:

Formulations are provided at 0.005 to 0.9 mg siRNA/mL, 0.22 μm filtersterilized in crimp top vials.

Formulation Details:

-   -   1. Lipid composition “1|57 Citrate blend” used in this study is        1.4:57.1:7.1:34.3 as described in molar percentages of        PEG-C-DMA, DLinDMA, DPPC, and cholesterol (in that order). This        formulation has an input lipid to drug ratio of 8.9.    -   2. Gear pump set up included 0.8 mm T-connector and 400 mL/min        speed.    -   3. siRNA used in this study is apoB-10048 U2/2 G1/2 siRNA.

Formulation Summary:

Particle Size 1:57 (9:1) + Zavg % Final L:D DOW siRNA (nm) Poly Encap(mg:mg) 322-050807-1 Syringe PBS Blend 79 0.12 92 13.6 322-050807-2Syringe Citrate 86 0.11 91 11.0 Blend 322-050807-3 Gear PBS Blend 800.09 93 11.3Procedures

Treatment: Just prior to the first treatment, animals are weighed anddose amounts are calculated based on the weight of individual animals(equivalent to 10 mL/kg, rounded to the nearest 10 μl). Test article isadministered by IV injection through the tail vein once on Day 0 (1 dosetotal per animal). Body weight is measured daily (every 24 h) for theduration of the study. Cage-side observations are taken daily in concertwith body weight measurements and additionally as warranted.

Group 1-7 Endpoint: Animals are sacrificed on Day 1, 24 h after testarticle administration. Blood is collected by cardiac puncture uponsacrifice. Whole amount is collected into a SST microtainer for serum.Clot for 30 (to 60) min at room temp., centrifuge for 5 min at 16,000×g& 16° C., invert to confirm centrifugation is complete, and store at 4°C. Analyze complete small-animal clinical chemistry panel plus AST andSDH. Top priority list: ALT, AST, SDH, Bilirubin, Alkaline Phosphatase,GGT, BUN, CPK, Glucose. Secondary priority list: Creatinine, Albumin,Globulin, Total Protein.

Group 8-12 Endpoint: Animals are sacrificed on Day 2, 48 h after testarticle administration. Blood is collected by cardiac puncture andprocessed for plasma. Immediately centrifuge for 5 min at 16,000×g (at16° C.). Record any observations of unusual plasma appearance. Pipetteoff clear plasma supernatant into a clean microfuge tube and store at−80° C. The following tissues are removed and weighed separately: liverand spleen. The bottom (unattached) half of the left liver lobe isdetached and submerged in ≧5 volumes of RNAlater (<0.3 g in 1.5 mLRNAlater in 2.0 mL tube), stored at least 16 hours at 4° C. prior toanalysis and long term storage at −20° C. or −80° C. for archivalpurposes. Formulations are expected to be well tolerated. Mice whichexhibit signs of distress associated with the treatment are terminatedat the discretion of the vivarium staff.

Termination: Mice are anaesthetized with a lethal dose ofketamine/xylazine; then cardiac puncture is performed followed bycervical dislocation.

Data Analysis: Tolerability of treatment regime is monitored by animalappearance and behavior as well as body weight. Blood clinical chemistryis measured by automated analyzer. ApoB and GAPDH mRNA levels in liverare measured via QG assay. ApoB protein in plasma is measured via ELISA.Total cholesterol in plasma is measured via standardenzymatic/colorimetric assay.

Results

There was no body weight loss or change in animal appearance/behaviorupon administration of the 1:57 SNALP formulations. FIG. 6 shows thatthe tolerability of SNALP prepared by citrate buffer versus PBS directdilution did not differ significantly in terms of blood clinicalchemistry parameters. There was a tolerability difference betweensyringe citrate and syringe PBS at constant siRNA dosage, but that waslikely an artifact dependent on the different final lipid:drug (L:D)ratios of these two preparations.

FIG. 7 shows that the efficacy of the 1:57 SNALP prepared by gear pumpwas similar to the same SNALP prepared by syringe press. Thetolerability profile was improved with the gear pump process, whichcould be attributed to increased initial encapsulation rate anddecreased final L:D ratio.

Example 8 In Vivo Silencing of ApoB Expression Using 1:57 SNALP PreparedVia a Direct Dilution or in-Line Dilution Process

This study illustrates a comparison of the tolerability and efficacy ofthe 1:57 SNALP formulation with ApoB-targeting siRNA as prepared by adirect dilution or in-line dilution process at an input lipid to drugratio of 6:1 or 9:1.

Experimental Design

Animal Model: Female BALB/c mice, 7 wks old.

siRNA payload: ApoB10048 U2/2 G1/2 siRNA.

CBC/Diff

# IV Dosage Group Mice Test Article Encap. siRNA Total Lipid 1 3 PBS — —2 3 1|57 SNALP (9:1)  7 mg/kg  71 mg/kg 3 3 1|57 SNALP (9:1) 11 mg/kg112 mg/kgClinical Chemistry:

# IV Dosage Group Mice Test Article Encap. siRNA Total Lipid 4 4 PBS — —5 4 1|57 SNALP (9:1)  9 mg/kg  92 mg/kg 6 4 1|57 SNALP (9:1) 11 mg/kg112 mg/kg 7 4 (6:1) New 1|57 SNALP 11 mg/kg  78 mg/kg 8 4 (6:1) New 1|57SNALP 13 mg/kg  93 mg/kg 9 4 (6:1) New 1|57 SNALP 15 mg/kg 107 mg/kg 104 (6:1) New 1|57 SNALP 17 mg/kg 121 mg/kg 11 4 1|57 SNALP (9:1) 11 mg/kg112 mg/kgActivity:

# IV Dosage Group Mice Test Article Encap. siRNA Total Lipid 12 4 PBS —— 13 4 1|57 SNALP (9:1) 0.05 mg/kg  0.51 mg/kg 14 4 1|57 SNALP (9:1) 0.1mg/kg 1.02 mg/kg 15 4 1|57 SNALP (9:1) 0.2 mg/kg 2.04 mg/kg 16 4 (6:1)New 1|57 SNALP 0.05 mg/kg  0.36 mg/kg 17 4 (6:1) New 1|57 SNALP 0.1mg/kg 0.71 mg/kg 18 4 (6:1) New 1|57 SNALP 0.2 mg/kg 1.42 mg/kg 19 4(6:1) New 1|57 SNALP 0.4 mg/kg 2.85 mg/kgFormulation:

Formulations are provided at 0.005 to 1.7 mg siRNA/mL, 0.22 μm filtersterilized in crimp top vials.

Formulation Details:

-   -   1. “1|57 SNALP” used in this study is lipid composition        1.4:57.1:7.1:34.3 as described in molar percentages of        PEG-C-DMA, DLinDMA, DPPC, and cholesterol (in that order). This        formulation was prepared by gear pump at an input lipid to drug        ratio of 9:1 (28 mM lipids) or 6:1 (14 mM lipids).    -   2. siRNA used in this study is apoB-10048 U2/2 G1/2 siRNA.

Formulation Summary:

Particle Size 1|57 SNALP Zavg % Final L:D Gear PBS In-Line (nm) PolyEncap (mg:mg) 322-051407-1 Input 9:1 78 0.07 93 10.2 322-051407-2 Input6:1 81 0.05 92 7.1Procedures

Treatment: Just prior to the first treatment, animals are weighed anddose amounts are calculated based on the weight of individual animals(equivalent to 10 mL/kg, rounded to the nearest 10 μl). Test article isadministered by IV injection through the tail vein once on Day 0 (1 dosetotal per animal). Body weight is measured daily (every 24 h) for theduration of the study. Cage-side observations are taken daily in concertwith body weight measurements and additionally as warranted.

Endpoint: Animals are sacrificed on Day 1, 24 h after test articleadministration (Grps 1-10) or on Day 2, 48 h after test articleadministration (Grps 11-19).

Groups 1-3: Blood is collected by cardiac puncture upon sacrifice. Wholeamount is collected into an EDTA microtainer, mixed immediately toprevent coagulation, and sent for analysis of CBC/Diff profile. Performbrief necropsy.

Groups 4-11: Blood is collected by cardiac puncture into a SSTmicrotainer for serum. Clot for 30 (to 60) min at room temp., centrifugefor 5 min at 16,000×g & 16° C., invert to confirm centrifugation iscomplete, and store at 4° C. Analyze complete small-animal clinicalchemistry panel plus AST and SDH. Top priority list: ALT, AST, SDH,Bilirubin, Alkaline Phosphatase, GGT, BUN, CPK, Glucose. Secondarypriority list: Creatinine, Albumin, Globulin, Total Protein. Performbrief necropsy.

Groups 12-19: Blood is collected by cardiac puncture and processed forplasma: immediately centrifuge for 5 min at 16,000×g (at 16° C.). Recordany observations of unusual plasma appearance. Pipette off clear plasmasupernatant into a clean microfuge tube and store at −80° C. Thefollowing tissues are removed: liver. The liver is not weighed; thebottom (unattached) half of the left liver lobe is detached andsubmerged in ≧5 volumes of RNAlater (<0.3 g in 1.5 mL RNAlater in 2.0 mLtube), stored at least 16 hours at 4° C. prior to analysis and long termstorage at −80° C. Formulations are expected to be well tolerated. Micewhich exhibit signs of distress associated with the treatment areterminated at the discretion of the vivarium staff.

Termination: Mice are anaesthetized with a lethal dose ofketamine/xylazine; then cardiac puncture is performed followed bycervical dislocation.

Data Analysis: Tolerability of treatment regime is monitored by animalappearance and behavior, and body weight. Blood clinical chemistry andCBC/Diff profile is measured by automated analyzer. Liver ApoB mRNA ismeasured using the QuantiGene Assay.

Plasma ApoB-100 is measured using ELISA. Plasma total cholesterol ismeasured using a standard enzymatic assay.

Results

Tolerability:

FIG. 8 shows that there was very little effect on body weight 24 hoursafter 1:57 SNALP administration. The maximum weight loss of 3.6±0.7% wasobserved at the highest drug dose of 17 mg/kg. There was also no obviouschange in animal appearance/behavior at any of the dosages tested.

FIG. 9 shows that there were no obvious changes in platelet count.Reduction of platelets can cause the mean platelet volume to increase asthe body produces new platelets in compensation for thetreatment-related decrease. Under the conditions of this study, the meanplatelet volume did not change in SNALP-treated groups.

FIG. 10 shows that clinically significant liver enzyme elevations(3×ULN) occurred at drug dosages of 11 mg/kg for 1:57 SNALP at alipid:drug (L:D) ratio of 10, and at 13 mg/kg at a L:D of 7. A slightdose response trend upwards in plasma total protein and globulin wasalso observed.

Efficacy:

FIG. 11 shows that based on the liver mRNA QuantiGene analysis, thepotency of the lower L:D SNALP was as good as that of the higher L:DSNALP at the tested drug dosages. In fact, the ApoB silencing activitywas identical at the 0.05 and 0.1 mg/kg dosages. As such, the potency ofthe 1:57 SNALP at a 6:1 input L:D ratio (final ratio of 7:1) was similarto the potency of the 1:57 SNALP at a 9:1 input L:D ratio (final ratioof 10:1) at reducing ApoB expression.

FIG. 12 shows that ApoB protein and total cholesterol levels werereduced to a similar extent by the 1:57 SNALP at a 6:1 input L:D ratio(final ratio of 7:1) and the 1:57 SNALP at a 9:1 input L:D ratio (finalratio of 10:1).

Therapeutic Index:

This study demonstrates that both the 1:57 SNALP at a 6:1 input L:Dratio (final ratio of 7:1) and the 1:57 SNALP at a 9:1 input L:D ratio(final ratio of 10:1) caused about 60% ApoB liver mRNA silencing with adrug dose of 0.1 mg/kg. Interpolating from the available data points inFIG. 10, a 10:1 final L:D ratio at 10 mg/kg may cause a similar degreeof enzyme elevation as a 7:1 final L:D ratio at 13 mg/kg. Using theseactivity and toxicity points, the therapeutic index for the 1:57 SNALPat a 10:1 final L:D ratio is (10 mg/kg)/(0.1 mg/kg)=100 and thetherapeutic index for the 1:57 SNALP at a 7:1 final L:D ratio is (13mg/kg)/(0.1 mg/kg)=130. Using this dataset, the therapeutic index forthe 1:57 SNALP at a 7:1 final L:D ratio is 30% greater than thetherapeutic index for the 1:57 SNALP at a 10:1 final L:D ratio.

Example 9 In Vivo Silencing of PLK-1 Expression Using 1:57 SNALPIncreases Survival of Hep3B Tumor-Bearing Mice

SNALP containing polo-like kinase 1 (PLK-1) siRNA (1:57 SNALPformulation: 1.4% PEG-cDMA; 57.1% DLinDMA; 7.1% DPPC; and 34.3%cholesterol) were tested for their effects on the survival of CD1 nu/numice bearing Hep3B liver tumors. PLK-1 is a serine/threonine kinasecontaining two functional domains: (1) a kinase domain; and (2) apolo-box domain (see, e.g., Barr et al., Nat. Rev. Mol. Cell. Biol.,5:429-440 (2004)). The activity and cellular concentration of PLK-1 arecrucial for the precise regulation of cell division. PLK-1 isoverexpressed in many cancer types including hepatoma and colon cancer,and PLK-1 expression often correlates with poor patient prognosis.Overexpression of PLK-1 (wild-type or kinase inactive) results inmultinucleation (genetic instability). Hyperactive PLK-1 overrides theDNA damage checkpoint. Constitutive PLK-1 expression causestransformation of NIH 3T3 cells. PLK-1 phosphorylates the p53 tumorsuppressor, thereby inhibiting the pro-apoptotic effects of p53. ThePLK-1 siRNA used in this study are provided in Table 8. Themodifications involved introducing 2′OMe-uridine or 2′OMe-guanosine atselected positions in the sense and antisense strands of the PLK-1 siRNAsequence, in which the siRNA duplex contained less than about 20%2′OMe-modified nucleotides.

TABLE 8 siRNA duplexes comprising sense andantisense PLK-1 RNA polynucleotides. SEQ ID % Modified in siRNAPLK-1 siRNA Sequence NO: DS Region PLK1424 U4/GU   5′-AGA U CACCC U CCUU AAA U ANN-3′ 5 6/38 = 15.8% 3′-NNUC U AGUGGGAG G AAUUUAU-5′ 6PLK1424 U4/G   5′-AGA U CACCC U CCU U AAA U ANN-3′ 5 7/38 = 18.4%3′-NNUCUA G UG G GA G GAAUUUAU-5′ 7 Column 1: The number after “PLK”refers to the nucleotide position of the 5′base of the sense strandrelative to the start codon (ATG) of the human PLK-1 mRNA sequenceNM_005030. Column 2: 2′-O-methyl (2′OMe) nucleotides are indicated inbold and underlined. The siRNA duplex can alternatively or additionallycomprise 2′-deoxy-2 ′-fluoro (2 ′F) nucleotides, 2′-deoxy nucleotides,2′-O-(2-methoxyethyl) (MOE) nucleotides, and/or locked nucleic acid(LNA) nucleotides. N = deoxythymidine (dT) nucleotide, uridine (U)ribonucleotide, or ribonucleotide having complementarity to the targetsequence (antisense strand) or the complementary strand thereof (sensestrand). Column 3: The number and percentage of modified nucleotides inthe double-stranded (DS) region of the siRNA duplex are provided.Experimental Groups

20 CD1 nu/nu mice were seeded as follows:

# Tumor # SNALP SNALP Group Mice seeding SNALP Mice dosing IV doseSacrifice Assay A 20 to I.H. Luc 1:57 9 Days 11, 14, 10 × 2 WhenSurvival B seed 1.5 × 10⁶ PLK 1424 1:57 9 17, 21, 25, 28, mg/kg moribundBody Weights Hep3B 32, 35, 39, 42Test Articles

All samples were filter-sterilized prior to dilution to workingconcentration. All tubes were labeled with the formulation date, lipidcomposition, and nucleic acid concentration. SNALP samples were providedat 0.2 mg/ml nucleic acid. A minimum of 20 ml of each SNALP was requiredto perform the study. Formulations for this study contained:

Group Test Article Description A Luc U/U SNALP 1:57 (28 mM lipid) BPLK1424 U4/GU SNALP 1:57 (28 mM lipid) PLK1424 U4/G SNALP 1:57 (28 mMlipid)Procedures

-   Day 0 Mice will receive Anafen by SC injection (100 μg in 20 μl    saline) immediately prior to surgery. Individual mice are    anesthetized by isoflourane gas inhalation and eye lube applied to    prevent excessive eye drying. While maintained under gas anesthesia    from a nose cone, a single 1.5 cm incision across the midline will    be made below the sternum. The left lateral hepatic lobe is then    exteriorized using an autoclaved cotton wool bud. 25 μl of tumor    cells suspended in PBS is injected into the lobe at a shallow angle    using a leur tip Hamilton syringe (50 μl) and 30 G (⅜″) needle.    Cells will be injected slowly (˜30 s) and a swab applied to the    puncture wound immediately after needle withdrawal. After any    bleeding has stopped (˜1 min), the incision is closed with 5-6    sutures in the muscle wall and 3-4 skin clips. Cell suspensions will    be thoroughly mixed immediately prior to each injection. Mice will    recover from anesthesia in a clean cage lined with paper towel and    monitored closely for 2-4 hours. Animals are then returned to normal    housing.-   Day 1 All mice will be lightly anesthetized by isoflourane gas and    the sutures examined. Animals will then receive Anafen by SC    injection (100 μg in 20 μl saline).-   Day 10 Mice will be randomized into the appropriate treatment    groups.-   Day 11 Groups A, B—Day 11: All Animals will be administered SNALP at    2 mg/kg by IV injection via the lateral tail vein. Mice will be    dosed according to body weight (10 ml/kg). Dosing will be repeated    for 5 consecutive days based on initial weight.-   Day 14-35 Groups A, B—Days 14, 17, 21, 25, 28, 32, 35: All Animals    will be re-administered SNALP at 2 mg/kg by IV injection via the    lateral tail vein. Mice will be dosed according to body weight (10    ml/kg).    -   Body weights Groups: Mice will be weighed on the day of dosing        for 5 weeks, then twice weekly until close of the study.    -   Endpoint: Tumor burden and formulations are expected to be well        tolerated. Mice that exhibit signs of distress associated with        the treatment or tumor burden are terminated at the discretion        of the vivarium staff.-   Termination: Mice are anesthetized with a lethal dose of    ketamine/xylazine followed by cervical dislocation.-   Data Analysis: Survival and body weights are assayed.    Results

FIG. 13 shows the mean body weights of mice during therapeutic dosing ofPLK1424 SNALP in the Hep3B intrahepatic (I.H.) tumor model. Thetreatment regimen was well tolerated with no apparent signs oftreatment-related toxicity.

FIG. 14 shows that treatment with 1:57 SNALP-formulated PLK1424 caused asignificant increase in the survival of Hep3B tumor-bearing mice. Thisin vivo anti-tumor effect was observed in the absence of any apparenttoxicity or immune stimulation.

Example 10 In Vivo Silencing of PLK-1 Expression Using 1:57 SNALPInduces Tumor Cell Apoptosis in Hep3B Tumor-Bearing Mice

The objectives of this study were as follows:

-   -   1. To determine the level of mRNA silencing in established Hep3B        liver tumors following a single IV administration of PLK1424        SNALP.    -   2. To confirm the mechanism of mRNA silencing by detecting        specific RNA cleavage products using RACE-PCR.    -   3. To confirm induction of tumor cell apoptosis by        histopathology.

The 1:57 SNALP formulation (1.4% PEG-cDMA; 57.1% DLinDMA; 7.1% DPPC; and34.3% cholesterol) was used for this study.

Experimental Groups

20 SCID/beige mice were seeded as follows:

# Tumor # SNALP Group Mice seeding SNALP Mice dosing IV Sacrifice AssayA 20 to I.H. PBS 6 1 × 2 mg/kg 24 h after Tumor QG B seed 1 × 10⁶ Luc1:57 7 Day 20 treatment Tumor RACE-PCR C Hep3B PLK 1424 1:57 7HistopathologyTest Articles

All samples were filter-sterilized prior to dilution to workingconcentration. All tubes were labeled with the formulation date, lipidcomposition, and nucleic acid concentration. SNALP samples were providedat 0.2 mg/ml nucleic acid. A minimum of 2 ml of SNALP was required toperform the study. Formulations for this study contained:

Group Test Article Description A PBS B Luc U/U 1:57 SNALP C PLK1424U4/GU 1:57 SNALPProcedures

-   Day 0 Mice will receive Anafen by SC injection (100 μg in 20 μl    saline) immediately prior to surgery. Individual mice are    anesthetized by isoflourane gas inhalation and eye lube applied to    prevent excessive eye drying. While maintained under gas anesthesia    from a nose cone, a single 1.5 cm incision across the midline will    be made below the sternum. The left lateral hepatic lobe is then    exteriorized using an autoclaved cotton wool bud. 25 μl of tumor    cells suspended in PBS is injected into the lobe at a shallow angle    using a leur tip Hamilton syringe (50 μl) and 30 G (⅜″) needle.    Cells will be injected slowly (˜30 s) and a swab applied to the    puncture wound immediately after needle withdrawal. After any    bleeding has stopped (˜1 min), the muscle wall incision is closed    with 5-6 sutures. The skin incision is then closed with 3-4 metal    skin clips. Cell suspensions will be thoroughly mixed immediately    prior to each injection. Mice will recover from anesthesia in a    clean cage lined with paper towel and monitored closely for 2-4    hours. Animals are then returned to normal housing.-   Day 1 All mice will be lightly anesthetized by isoflourane gas and    the sutures examined. Animals will then receive Anafen by SC    injection (100 μg in 20 μl saline).-   Day 7 Mice will be randomized into the appropriate treatment groups.-   Day 20 Groups A-C: Mice will be weighed and then administered either    PBS, Luc, or PLK1424 SNALP by IV injection via the lateral tail    vein. SNALP will be dosed at 2 mg/kg or equivalent volume (10 ml/kg)    according to body weight.-   Day 21 Groups A-C: All mice will be weighed and then euthanized by    lethal anesthesia.    -   Tumor bearing liver lobes from all mice in each group will be        weighed and collected into RNALater for RNA analysis.    -   Endpoint: Tumor burden and formulations are expected to be well        tolerated. Mice that exhibit signs of distress associated with        the treatment or tumor burden are terminated at the discretion        of the vivarium staff.-   Termination: Mice are anaesthetized with a lethal dose of    ketamine/xylazine followed by cervical dislocation.-   Data Analysis: mRNA analysis of liver tumors by bDNA (QG) assay and    RACE-PCR.    -   Tumor cell apoptosis by histopathology.        Results

Body weights were monitored from Day 14 onwards to assess tumorprogression. On Day 20, 6 mice showing greatest weight loss wererandomized into each of the 3 groups and treated. All six mice hadsubstantial-large I.H. tumors at sacrifice (Day 21). Treatment of theremaining 14 mice was therefore initiated on the Day 21 (sacrifice Day22). 10/14 mice had substantial tumors; 2/14 mice had small/probabletumors; and 2/14 mice had no visible tumor burden.

FIG. 15 shows data from Quantigene assays used to measure human(tumor)-specific PLK-1 mRNA levels. A single 2 mg/kg dose of 1:57 SNALPreduced PLK-1 mRNA levels by about 50% in intrahepatic Hep3B tumorsgrowing in mice.

FIG. 16 shows that a specific cleavage product of PLK-1 mRNA wasdetectable in mice treated with PLK1424 SNALP by 5′ RACE-PCR. Nospecific PCR product was detectable in mice treated with either PBS orcontrol (Luc) SNALP. Nucleotide sequencing of the PCR product confirmedthe predicted cleavage site by PLK1424 siRNA-mediated RNA interferencein the PLK-1 mRNA.

FIG. 17 shows Hep3B tumor histology in mice treated with either LucSNALP (top) or PLK1424 SNALP (bottom). Luc SNALP-treated mice displayednormal mitoses in Hep3B tumors, whereas PLK1424 SNALP-treated miceexhibited numerous aberrant mitoses and tumor cell apoptosis in Hep3Btumors.

CONCLUSION

This example illustrates that a single administration of PLK1424 1:57SNALP to Hep3B tumor-bearing mice induced significant in vivo silencingof PLK-1 mRNA. This reduction in PLK-1 mRNA was confirmed to be mediatedby RNA interference using 5′ RACE-PCR analysis. Importantly, PLK-1 mRNAsilencing by the 1:57 SNALP formulation profoundly disrupted tumor cellproliferation (mitosis), causing subsequent apoptosis of tumor cells. Asdemonstrated in the previous example, this anti-tumor effect translatedinto extended survival times in the tumor-bearing mice.

Example 11 Comparison of 1:57 PLK-1 SNALP Containing Either PEG-cDMA orPEG-cDSA in a Subcutaneous Hep3B Tumor Model

This example demonstrates the utility of the PEG-lipid PEG-cDSA(3-N—[(-Methoxypoly(ethyleneglycol)2000)carbamoyl]-1,2-distearyloxypropylamine) in the 1:57formulation for systemically targeting distal (e.g., subcutaneous)tumors. In particular, this example compares the tumor targeting abilityof 1:57 PLK-1 SNALPs containing either PEG-cDMA (C₁₄) or PEG-cDSA (C₁₈).Readouts are tumor growth inhibition and PLK1 mRNA silencing. The PLK-1siRNA used was PLK1424 U4/GU, the sequence of which is provided in Table8.

Subcutaneous (S.C.) Hep3B tumors were established in scid/beige mice.Multidose anti-tumor efficacy of 1:57 PLK-1 SNALP was evaluated for thefollowing groups (n=5 for each group): (1) “Luc-cDMA”-PEG-cDMA LucSNALP; (2) “PLK-cDMA”-PEG-cDMA PLK-1 SNALP; and (3) “PLK-cDSA”-PEG-cDSAPLK-1 SNALP. Administration of 6×2 mg/kg siRNA was initiated once tumorsreached about 5 mm in diameter (Day 10). Dosing was performed on Days10, 12, 14, 17, 19, and 21. Tumors were measured by caliper twiceweekly.

FIG. 18 shows that multiple doses of 1:57 PLK-1 SNALP containingPEG-cDSA induced the regression of established Hep3B S.C. tumors. Inparticular, 5/5 tumors in the PLK1-cDSA treated mice appeared flat,measurable only by discoloration at the tumor site.

FIG. 19 shows the mRNA silencing of 1:57 PLK SNALP in S.C. Hep3B tumorsfollowing a single intravenous SNALP administration. The extent ofsilencing observed with the PLK1-cDSA SNALP correlated with theanti-tumor activity in the multi-dose study shown in FIG. 18.

The Luc-cDMA SNALP-treated group, which had developed large S.C. tumorsat Day 24, were then administered PLK-cDSA SNALP on Days 24, 26, 28, 31,33, and 35. There was no additional dosing of the original PLK-1SNALP-treated groups. The results from this crossover dosing study withlarge established tumors is provided in FIG. 20, which shows thatPLK1-cDSA SNALP inhibited the growth of large S.C. Hep3B tumors.

A comparison of the effect of PEG-cDMA and PEG-cDSA 1:57 SNALPs on PLK-1mRNA silencing was performed using established intrahepatic Hep3B tumorsin scid/beige mice. A single 2 mg/kg dose of 1:57 PLK-1 SNALP containingeither PEG-cDMA or PEG-cDSA was administered intravenously. Liver/tumorsamples were collected at 24 and 96 hours after SNALP treatment.Control=2 mg/kg Luc-cDMA SNALP at 24 hours.

FIG. 21 shows that PLK-cDMA SNALP and PLK-cDSA SNALP had similarsilencing activities after 24 hours, but that the PLK-cDSA SNALP mayincrease the duration of mRNA silencing in intrahepatic tumors.

FIG. 22 shows the blood clearance profile of 1:57 PLK-1 SNALP containingeither PEG-cDMA or PEG-cDSA. The extended blood circulation timesobserved for the PLK-cDSA SNALP may enable the increased accumulationand activity at distal (e.g., subcutaneous) tumor sites.

Thus, this study shows that the 1:57 PEG-cDSA SNALP formulation can beused to preferentially target tumors outside of the liver, whereas the1:57 PEG-cDMA SNALP can be used to preferentially target the liver.

Example 12 Synthesis of Cholesteryl-2′-Hydroxyethyl Ether

Step 1: A 250 ml round bottom flask containing cholesterol (5.0 g, 12.9mmol) and a stir bar was sealed and flushed with nitrogen.Toluenesulphonyl chloride (5.0 g, 26.2 mmol) was weighed into a separate100-mL round bottom flask, also sealed and flushed with nitrogen.Anhydrous pyridine (2×50 ml) was delivered to each flask. Thetoluenesulphonyl chloride solution was then transferred, via cannula,into the 250 ml flask, and the reaction stirred overnight. The pyridinewas removed by rotovap, and methanol (80 ml) added to the residue. Thiswas then stirred for 1 hour until a homogeneous suspension was obtained.The suspension was filtered, washed with acetonitrile (50 ml), and driedunder vacuum to yield cholesteryl tosylate as a fluffy white solid (6.0g, 86%).

Step 2: Cholesteryl tosylate (2.0 g, 3.7 mmol), 1,4-dioxane (50 mL), andethylene glycol (4.6 g, 74 mmol) were added to a 100 ml flask containinga stir bar. The flask was fitted with a condenser, and refluxedovernight. The dioxane was then removed by rotovap, and the reactionmixture suspended in water (100 ml). The solution was transferred to aseparating funnel and extracted with chloroform (3×100 ml). The organicphases were combined, washed with water (2×150 ml), dried over magnesiumsulphate, and the solvent removed. The crude product was purified bycolumn chromatography (5% acetone/hexane) to yield the product as awhite solid (1.1 g, 69%).

The structures of the cholesterol derivativescholesteryl-2′-hydroxyethyl ether and cholesteryl-4′-hydroxybutyl etherare as follows:

It is to be understood that the above description is intended to beillustrative and not restrictive. Many embodiments will be apparent tothose of skill in the art upon reading the above description. The scopeof the invention should, therefore, be determined not with reference tothe above description, but should instead be determined with referenceto the appended claims, along with the full scope of equivalents towhich such claims are entitled. The disclosures of all articles andreferences, including patent applications, patents, PCT publications,and Genbank Accession Nos., are incorporated herein by reference for allpurposes.

1. A nucleic acid-lipid particle comprising: (a) a nucleic acid; (b) acationic lipid comprising from 50 mol % to 65 mol % of the total lipidpresent in the particle; (c) a non-cationic lipid comprising a mixtureof a phospholipid and cholesterol or a derivative thereof, wherein thephospholipid comprises from 4 mol % to 10 mol % of the total lipidpresent in the particle and the cholesterol or derivative thereofcomprises from 30 mol % to 40 mol % of the total lipid present in theparticle; and (d) a conjugated lipid that inhibits aggregation ofparticles comprising from 0.5 mol % to 2 mol % of the total lipidpresent in the particle.
 2. The nucleic acid-lipid particle of claim 1,wherein the nucleic acid comprises a small interfering RNA (siRNA). 3.The nucleic acid-lipid particle of claim 2, wherein the siRNA comprisesfrom about 15 to about 60 nucleotides.
 4. The nucleic acid-lipidparticle of claim 2, wherein the siRNA comprises at least one modifiednucleotide.
 5. The nucleic acid-lipid particle of claim 2, wherein thesiRNA comprises at least one 2′-O-methyl (2′OMe) nucleotide.
 6. Thenucleic acid-lipid particle of claim 2, wherein said siRNA is about 19to about 25 base pairs in length.
 7. The nucleic acid-lipid particle ofclaim 2, wherein said siRNA comprises 3′ overhangs.
 8. The nucleicacid-lipid particle of claim 1, wherein the cationic lipid comprisesfrom 52 mol % to 62 mol % of the total lipid present in the particle. 9.The nucleic acid-lipid particle of claim 1, wherein the phospholipidcomprises dipalmitoylphosphatidylcholine (DPPC),distearoylphosphatidylcholine (DSPC), or a mixture thereof.
 10. Thenucleic acid-lipid particle of claim 1, wherein the conjugated lipidthat inhibits aggregation of particles comprises a polyethyleneglycol(PEG)-lipid conjugate.
 11. The nucleic acid-lipid particle of claim 10,wherein the PEG-lipid conjugate comprises a PEG-diacylglycerol (PEG-DAG)conjugate, a PEG-dialkyloxypropyl (PEG-DAA) conjugate, or a mixturethereof.
 12. The nucleic acid-lipid particle of claim 11, wherein thePEG-DAA conjugate comprises a PEG-dimyristyloxypropyl (PEG-DMA)conjugate, a PEG-distearyloxypropyl (PEG-DSA) conjugate, or a mixturethereof.
 13. The nucleic acid-lipid particle of claim 12, wherein thePEG has an average molecular weight of about 2,000 daltons.
 14. Thenucleic acid-lipid particle of claim 10, wherein the nucleic acid-lipidparticle comprises about 57.1 mol % cationic lipid, about 7.1 mol %phospholipid, about 34.3 mol % cholesterol or a derivative thereof, andabout 1.4 mol % PEG-lipid conjugate.
 15. The nucleic acid-lipid particleof claim 1, wherein the conjugated lipid that inhibits aggregation ofparticles comprises from 1 mol % to 2 mol % of the total lipid presentin the particle.
 16. The nucleic acid-lipid particle of claim 1, whereinthe nucleic acid in the nucleic acid-lipid particle is not substantiallydegraded after incubation of the particle in serum at 37° C. for 30minutes.
 17. The nucleic acid-lipid particle of claim 1, wherein thenucleic acid is fully encapsulated in the nucleic acid-lipid particle.18. The nucleic acid-lipid particle of claim 1, wherein the nucleicacid-lipid particle has a lipid:nucleic acid mass ratio of from about 5to about
 15. 19. The nucleic acid-lipid particle of claim 1, wherein thenucleic acid-lipid particle has a median diameter of from about 40 nm toabout 150 nm.
 20. The nucleic acid-lipid particle of claim 1, whereinthe phospholipid comprises from 5 mol % to 9 mol % of the total lipidpresent in the particle.
 21. The nucleic acid-lipid particle of claim 1,wherein the cholesterol or derivative thereof comprises from 32 mol % to36 mol % of the total lipid present in the particle.
 22. Apharmaceutical composition comprising a nucleic acid-lipid particle ofclaim 1 and a pharmaceutically acceptable carrier.